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Antwi-Boasiako A, Jia S, Liu J, Guo N, Chen C, Karikari B, Feng J, Zhao T. Identification and Genetic Dissection of Resistance to Red Crown Rot Disease in a Diverse Soybean Germplasm Population. PLANTS (BASEL, SWITZERLAND) 2024; 13:940. [PMID: 38611470 PMCID: PMC11013609 DOI: 10.3390/plants13070940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 03/18/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024]
Abstract
Red crown rot (RCR) disease caused by Calonectria ilicicola negatively impacts soybean yield and quality. Unfortunately, the knowledge of the genetic architecture of RCR resistance in soybeans is limited. In this study, 299 diverse soybean accessions were used to explore their genetic diversity and resistance to RCR, and to mine for candidate genes via emergence rate (ER), survival rate (SR), and disease severity (DS) by a multi-locus random-SNP-effect mixed linear model of GWAS. All accessions had brown necrotic lesions on the primary root, with five genotypes identified as resistant. Nine single-nucleotide polymorphism (SNP) markers were detected to underlie RCR response (ER, SR, and DS). Two SNPs colocalized with at least two traits to form a haplotype block which possessed nine genes. Based on their annotation and the qRT-PCR, three genes, namely Glyma.08G074600, Glyma.08G074700, and Glyma.12G043600, are suggested to modulate soybean resistance to RCR. The findings from this study could serve as the foundation for breeding RCR-tolerant soybean varieties, and the candidate genes could be validated to deepen our understanding of soybean response to RCR.
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Affiliation(s)
- Augustine Antwi-Boasiako
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (A.A.-B.); (S.J.); (J.L.); (N.G.)
- Council for Scientific and Industrial Research-Crops Research Institute (CSIR-CRI), Fumesua, Kumasi P.O. Box 3785, Ghana
| | - Shihao Jia
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (A.A.-B.); (S.J.); (J.L.); (N.G.)
| | - Jiale Liu
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (A.A.-B.); (S.J.); (J.L.); (N.G.)
| | - Na Guo
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (A.A.-B.); (S.J.); (J.L.); (N.G.)
| | - Changjun Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China;
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale P.O. Box TL 1882, Ghana;
- Département de Phytologie, Université Laval, Québec, QC G1V 0A6, Canada
| | - Jianying Feng
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (A.A.-B.); (S.J.); (J.L.); (N.G.)
| | - Tuanjie Zhao
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (A.A.-B.); (S.J.); (J.L.); (N.G.)
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Abdelraheem A, Zhu Y, Zeng L, Stetina S, Zhang J. A genome-wide association study for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in diploid cotton (Gossypium arboreum) and resistance transfer to tetraploid Gossypium hirsutum. Mol Genet Genomics 2024; 299:30. [PMID: 38472439 DOI: 10.1007/s00438-024-02130-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024]
Abstract
Fusarium wilt, caused by the soilborne fungus Fusarium oxysporum f. sp. vasinfectum (FOV), is a devastating disease affecting cotton (Gossypium spp.) worldwide. Understanding the genetic basis of resistance in diploid cotton and successfully transferring the resistance to tetraploid Upland cotton (G. hirsutum) are crucial for developing resistant cotton cultivars. Although numerous studies have been conducted to investigate the genetic basis of Fusarium wilt in tetraploid cotton, little research has been conducted on diploid species. In this study, an association mapping panel consisting of 246 accessions of G. arboreum, was used to identify chromosomal regions for FOV race 4 (FOV4) resistance based on foliar disease severity ratings in four greenhouse tests. Through a genome-wide association study (GWAS) based on 7,009 single nucleotide polymorphic (SNP) markers, 24 FOV4 resistance QTLs, including three major QTLs on chromosomes A04, A06, and A11, were detected. A validation panel consisting of 97 diploid cotton accessions was employed, confirming the presence of several QTLs. Evaluation of an introgressed BC2F7 population derived from G. hirsutum/G. aridum/G. arboreum showed significant differences in disease incidence and mortality rate, as compared to susceptible and resistant controls, suggesting that the resistance in G. arboreum and/or G. aridum was transferred into Upland cotton for the first time. The identification of novel major resistance QTLs, along with the transfer of resistance from the diploid species, expands our understanding of the genomic regions involved in conferring resistance to FOV4 and contributes to the development of resilient Upland cotton cultivars.
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Affiliation(s)
- Abdelraheem Abdelraheem
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Yi Zhu
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Linghe Zeng
- USDA Agricultural Research Service Crop Genetics Research Unit, Stoneville, MS, 38776, USA
| | - Salliana Stetina
- USDA Agricultural Research Service Crop Genetics Research Unit, Stoneville, MS, 38776, USA
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
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Neves NODS, De Dea Lindner J, Stockhausen L, Delziovo FR, Bender M, Serzedello L, Cipriani LA, Ha N, Skoronski E, Gisbert E, Sanahuja I, Perez Fabregat TEH. Fermentation of Plant-Based Feeds with Lactobacillus acidophilus Improves the Survival and Intestinal Health of Juvenile Nile Tilapia ( Oreochromis niloticus) Reared in a Biofloc System. Animals (Basel) 2024; 14:332. [PMID: 38275792 PMCID: PMC10812702 DOI: 10.3390/ani14020332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
This study evaluated the effect of fermentation with Lactobacillus acidophilus on the biochemical and nutritional compositions of a plant-based diet and its effects on the productive performance and intestinal health of juvenile Nile tilapia (Oreochromis niloticus) reared in a biofloc technology (BFT) system. The in vitro kinetics of feed fermentation were studied to determine the L. acidophilus growth and acidification curve through counting the colony-forming units (CFUs) mL-1 and measuring the pH. Physicochemical and bromatological analyses of the feed were also performed. Based on the microbial growth kinetics results, vegetable-based Nile tilapia feeds fermented for 6 (FPB6) and 18 (FPB18) h were evaluated for 60 days. Fermented diets were compared with a positive control diet containing fishmeal (CFM) and a negative control diet without animal protein (CPB). Fermentation with L. acidophilus increased lactic acid bacteria (LAB) count and the soluble protein concentration of the plant-based feed, as well as decreasing the pH (p < 0.05). FPB treatments improved fish survival compared with CPB (p < 0.05). Fermentation increased feed intake but worsened feed efficiency (p < 0.05). The use of fermented feeds increased the LAB count and reduced pathogenic bacteria both in the BFT system's water and in the animals' intestines (p < 0.05). Fermented plant-based feeds showed greater villi (FPB6; FPB18) and higher goblet cell (FPB6) counts relative to the non-fermented plant-based feed, which may indicate improved intestinal health. The results obtained in this study are promising and show the sustainable potential of using fermented plant-based feeds in fish feeding rather than animal protein and, in particular, fishmeal.
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Affiliation(s)
- Nataly Oliveira Dos Santos Neves
- Department of Animal Science (Pisciculture), Universidade do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090, Bairro Conta Dinheiro, Lages 88520-000, SC, Brazil; (N.O.D.S.N.); (L.S.); (F.R.D.); (M.B.); (L.S.); (L.A.C.); (N.H.); (E.S.)
| | - Juliano De Dea Lindner
- Department of Food Science and Technology, Universidade Federal de Santa Catarina (UFSC), Rod. Admar Gonzaga, 1346, Bairro Itacorubi, Florianópolis 88034-000, SC, Brazil;
| | - Larissa Stockhausen
- Department of Animal Science (Pisciculture), Universidade do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090, Bairro Conta Dinheiro, Lages 88520-000, SC, Brazil; (N.O.D.S.N.); (L.S.); (F.R.D.); (M.B.); (L.S.); (L.A.C.); (N.H.); (E.S.)
| | - Fernanda Regina Delziovo
- Department of Animal Science (Pisciculture), Universidade do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090, Bairro Conta Dinheiro, Lages 88520-000, SC, Brazil; (N.O.D.S.N.); (L.S.); (F.R.D.); (M.B.); (L.S.); (L.A.C.); (N.H.); (E.S.)
| | - Mariana Bender
- Department of Animal Science (Pisciculture), Universidade do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090, Bairro Conta Dinheiro, Lages 88520-000, SC, Brazil; (N.O.D.S.N.); (L.S.); (F.R.D.); (M.B.); (L.S.); (L.A.C.); (N.H.); (E.S.)
| | - Letícia Serzedello
- Department of Animal Science (Pisciculture), Universidade do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090, Bairro Conta Dinheiro, Lages 88520-000, SC, Brazil; (N.O.D.S.N.); (L.S.); (F.R.D.); (M.B.); (L.S.); (L.A.C.); (N.H.); (E.S.)
| | - Luiz Augusto Cipriani
- Department of Animal Science (Pisciculture), Universidade do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090, Bairro Conta Dinheiro, Lages 88520-000, SC, Brazil; (N.O.D.S.N.); (L.S.); (F.R.D.); (M.B.); (L.S.); (L.A.C.); (N.H.); (E.S.)
| | - Natalia Ha
- Department of Animal Science (Pisciculture), Universidade do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090, Bairro Conta Dinheiro, Lages 88520-000, SC, Brazil; (N.O.D.S.N.); (L.S.); (F.R.D.); (M.B.); (L.S.); (L.A.C.); (N.H.); (E.S.)
| | - Everton Skoronski
- Department of Animal Science (Pisciculture), Universidade do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090, Bairro Conta Dinheiro, Lages 88520-000, SC, Brazil; (N.O.D.S.N.); (L.S.); (F.R.D.); (M.B.); (L.S.); (L.A.C.); (N.H.); (E.S.)
| | - Enric Gisbert
- Aquaculture Program, Institute of Agrifood Research and Technology (IRTA-La Ràpita), Ctra. Poble Nou. Km 5.5, 43540 La Ràpita, Spain;
| | - Ignasi Sanahuja
- Aquaculture Program, Institute of Agrifood Research and Technology (IRTA-La Ràpita), Ctra. Poble Nou. Km 5.5, 43540 La Ràpita, Spain;
| | - Thiago El Hadi Perez Fabregat
- Department of Animal Science (Pisciculture), Universidade do Estado de Santa Catarina (UDESC), Av. Luiz de Camões, 2090, Bairro Conta Dinheiro, Lages 88520-000, SC, Brazil; (N.O.D.S.N.); (L.S.); (F.R.D.); (M.B.); (L.S.); (L.A.C.); (N.H.); (E.S.)
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Sang Y, Liu X, Yuan C, Yao T, Li Y, Wang D, Zhao H, Wang Y. Genome-wide association study on resistance of cultivated soybean to Fusarium oxysporum root rot in Northeast China. BMC PLANT BIOLOGY 2023; 23:625. [PMID: 38062401 PMCID: PMC10702129 DOI: 10.1186/s12870-023-04646-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Fusarium oxysporum is a prevalent fungal pathogen that diminishes soybean yield through seedling disease and root rot. Preventing Fusarium oxysporum root rot (FORR) damage entails on the identification of resistance genes and developing resistant cultivars. Therefore, conducting fine mapping and marker development for FORR resistance genes is of great significance for fostering the cultivation of resistant varieties. In this study, 350 soybean germplasm accessions, mainly from Northeast China, underwent genotyping using the SoySNP50K Illumina BeadChip, which includes 52,041 single nucleotide polymorphisms (SNPs). Their resistance to FORR was assessed in a greenhouse. Genome-wide association studies utilizing the general linear model, mixed linear model, compressed mixed linear model, and settlement of MLM under progressively exclusive relationship models were conducted to identify marker-trait associations while effectively controlling for population structure. RESULTS The results demonstrated that these models effectively managed population structure. Eight SNP loci significantly associated with FORR resistance in soybean were detected, primarily located on Chromosome 6. Notably, there was a strong linkage disequilibrium between the large-effect SNPs ss715595462 and ss715595463, contributing substantially to phenotypic variation. Within the genetic interval encompassing these loci, 28 genes were present, with one gene Glyma.06G088400 encoding a protein kinase family protein containing a leucine-rich repeat domain identified as a potential candidate gene in the reference genome of Williams82. Additionally, quantitative real-time reverse transcription polymerase chain reaction analysis evaluated the gene expression levels between highly resistant and susceptible accessions, focusing on primary root tissues collected at different time points after F. oxysporum inoculation. Among the examined genes, only this gene emerged as the strongest candidate associated with FORR resistance. CONCLUSIONS The identification of this candidate gene Glyma.06G088400 improves our understanding of soybean resistance to FORR and the markers strongly linked to resistance can be beneficial for molecular marker-assisted selection in breeding resistant soybean accessions against F. oxysporum.
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Affiliation(s)
- Yongsheng Sang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, 130118, Jilin, PR China
- College of Agronomy, Jilin Agricultural University, Changchun, 130118, Jilin, PR China
| | - Xiaodong Liu
- Crop Germplasm Institute, Jilin Academy of Agricultural Sciences, Changchun, 130118, Jilin, China
| | - Cuiping Yuan
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, 130118, Jilin, PR China
| | - Tong Yao
- College of Agronomy, Jilin Agricultural University, Changchun, 130118, Jilin, PR China
| | - Yuqiu Li
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, 130118, Jilin, PR China
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A384-E, East Lansing, MI, 48824, USA
| | - Hongkun Zhao
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, 130118, Jilin, PR China.
| | - Yumin Wang
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, National Engineering Research Center for Soybean, Changchun, 130118, Jilin, PR China.
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Million CR, Wijeratne S, Karhoff S, Cassone BJ, McHale LK, Dorrance AE. Molecular mechanisms underpinning quantitative resistance to Phytophthora sojae in Glycine max using a systems genomics approach. FRONTIERS IN PLANT SCIENCE 2023; 14:1277585. [PMID: 38023885 PMCID: PMC10662313 DOI: 10.3389/fpls.2023.1277585] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
Expression of quantitative disease resistance in many host-pathogen systems is controlled by genes at multiple loci, each contributing a small effect to the overall response. We used a systems genomics approach to study the molecular underpinnings of quantitative disease resistance in the soybean-Phytophthora sojae pathosystem, incorporating expression quantitative trait loci (eQTL) mapping and gene co-expression network analysis to identify the genes putatively regulating transcriptional changes in response to inoculation. These findings were compared to previously mapped phenotypic (phQTL) to identify the molecular mechanisms contributing to the expression of this resistance. A subset of 93 recombinant inbred lines (RILs) from a Conrad × Sloan population were inoculated with P. sojae isolate 1.S.1.1 using the tray-test method; RNA was extracted, sequenced, and the normalized read counts were genetically mapped from tissue collected at the inoculation site 24 h after inoculation from both mock and inoculated samples. In total, more than 100,000 eQTLs were mapped. There was a switch from predominantly cis-eQTLs in the mock treatment to an almost entirely nonoverlapping set of predominantly trans-eQTLs in the inoculated treatment, where greater than 100-fold more eQTLs were mapped relative to mock, indicating vast transcriptional reprogramming due to P. sojae infection occurred. The eQTLs were organized into 36 hotspots, with the four largest hotspots from the inoculated treatment corresponding to more than 70% of the eQTLs, each enriched for genes within plant-pathogen interaction pathways. Genetic regulation of trans-eQTLs in response to the pathogen was predicted to occur through transcription factors and signaling molecules involved in plant-pathogen interactions, plant hormone signal transduction, and MAPK pathways. Network analysis identified three co-expression modules that were correlated with susceptibility to P. sojae and associated with three eQTL hotspots. Among the eQTLs co-localized with phQTLs, two cis-eQTLs with putative functions in the regulation of root architecture or jasmonic acid, as well as the putative master regulators of an eQTL hotspot nearby a phQTL, represent candidates potentially underpinning the molecular control of these phQTLs for resistance.
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Affiliation(s)
- Cassidy R. Million
- Department of Plant Pathology, The Ohio State University, Wooster, OH, United States
- Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
| | - Saranga Wijeratne
- Molecular and Cellular Imaging Center, The Ohio State University, Wooster, OH, United States
| | - Stephanie Karhoff
- Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Translational Plant Sciences Graduate Program, The Ohio State University, Columbus, OH, United States
| | - Bryan J. Cassone
- Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Department of Biology, Brandon University, Brandon, Manitoba, MB, Canada
| | - Leah K. McHale
- Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, United States
| | - Anne E. Dorrance
- Department of Plant Pathology, The Ohio State University, Wooster, OH, United States
- Center for Soybean Research and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, United States
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Simko I, Sthapit Kandel J, Peng H, Zhao R, Subbarao KV. Genetic determinants of lettuce resistance to drop caused by Sclerotinia minor identified through genome-wide association mapping frequently co-locate with loci regulating anthocyanin content. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:180. [PMID: 37548768 DOI: 10.1007/s00122-023-04421-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/12/2023] [Indexed: 08/08/2023]
Abstract
KEY MESSAGE GWAS identified 19 QTLs for resistance to Sclerotinia minor, 11 of them co-locating with red leaf color. Lower disease incidence was observed in red and dark red accessions. Lettuce (Lactuca sativa L.), one of the most economically important vegetables grown primarily in moderate climates around the world, is susceptible to many diseases including lettuce drop caused by the soilborne fungus Sclerotinia minor. Complete resistance to S. minor has not been identified in cultivated lettuce or its wild relatives. We conducted five experiments over 4 years with the diversity panel of almost 500 lettuce accessions to evaluate their response to the pathogen in an artificially infested field. The lowest disease incidence (DI) was observed in cultivars Eruption, Infantry, and Annapolis (median DI of 12.1-17.5%), while the highest DI was recorded for cultivars Reine des Glaces, Wayahead, and line FL. 43007 (median DI of 81.0-95.2%). Overall, significantly lower DI was observed in red and dark red accessions compared to those with a lower anthocyanin content. Genome-wide association mapping identified 19 QTLs for resistance to S. minor, 21 for the presence of red leaf color or its variations caused by the anthocyanin content, and one for the green color intensity. Eleven of the QTLs for disease resistance were located within 10 Mb of the loci associated with red color or anthocyanin content identified in this diversity panel. The frequent, non-random co-location of QTLs, together with the lower DI observed in red and dark red accessions suggests that lettuce interaction with S. minor may be partly influenced by anthocyanins. We have identified RLL2 and ANS, the genes of the anthocyanin biosynthesis pathway that co-locate with resistance QTLs, as candidates for functional studies to ascertain the involvement of anthocyanins in lettuce resistance against S. minor. Resistance QTLs closely linked with QTLs for anthocyanin content could be used to develop lettuce with a relatively high partial resistance and red color, while those not associated with anthocyanins could be used to develop partially resistant cultivars of green color.
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Affiliation(s)
- Ivan Simko
- Crop Improvement and Protection Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Salinas, CA, 93905, USA.
| | - Jinita Sthapit Kandel
- Edward T. Schafer Agricultural Research Center, U.S. Department of Agriculture, Agricultural Research Service, Fargo, ND, 58102, USA
| | - Hui Peng
- Everglades Research and Education Center, Horticultural Sciences Department, University of Florida, Belle Glade, FL, 33430, USA
| | - Rebecca Zhao
- Crop Improvement and Protection Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Salinas, CA, 93905, USA
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, c/o U.S., Agricultural Research Station, Salinas, CA, 93905, USA.
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Wang Y, Lu N, Wang K, Li Y, Zhang M, Liu S, Li Y, Zhou F. Fluxapyroxad Resistance Mechanisms in Sclerotinia sclerotiorum. PLANT DISEASE 2023; 107:1035-1043. [PMID: 36058635 DOI: 10.1094/pdis-07-22-1615-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The necrotrophic pathogen Sclerotinia sclerotiorum has a global distribution and a wide host range, making it one of the most damaging and economically important of all plant pathogens. The current study found that fluxapyroxad, a typical succinate dehydrogenase inhibitor fungicide, had a strong inhibitory effect against S. sclerotiorum, with mean effective concentration for 50% inhibition (EC50) values ranging from 0.021 to 0.095 µg/ml. Further investigation of five highly resistant S. sclerotiorum mutants, with EC50 values of 12.37 to 31.36 µg/ml, found that fluxapyroxad resistance was accompanied by a certain cost to fitness. All of the mutants were found to have significantly (P < 0.05) reduced mycelial growth and altered sclerotia production in artificial culture, as well as reduced pathogenicity, compared with wild-type isolates, with one mutant completely losing the capacity to infect detached soybean leaves. Sequence analysis demonstrated that four of the mutants had point mutations leading to amino acid changes in the SsSdhB subunit of the fungicide target protein succinate dehydrogenase. In addition, two of the mutants were also found to have amino acid changes in the predicted sequence of their SsSdhD subunit, while the fifth mutant had no changes in any of its SsSdh sequences, indicating that an alternative mechanism might be responsible for the observed resistance in this mutant. No cross-resistance was found between fluxapyroxad and any of the other fungicides tested, including tebuconazole, prochloraz, dimethachlone, carbendazim, procymidone, pyraclostrobin, boscalid, fluazinam, fludioxonil, and cyprodinil, which indicates that fluxapyroxad has great potential as an alternative method of control for the Sclerotinia stem rot caused by S. sclerotiorum, and which could provide ongoing protection to the soybean fields of China.
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Affiliation(s)
- Yanfen Wang
- School of Resources and Environment, Henan Institute of Science and Technology, Xinxiang 453003, China
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Ninghai Lu
- School of Resources and Environment, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Kuaikuai Wang
- School of Resources and Environment, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yinna Li
- School of Resources and Environment, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Mengli Zhang
- School of Resources and Environment, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Shuang Liu
- School of Resources and Environment, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yanling Li
- School of Resources and Environment, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Feng Zhou
- School of Resources and Environment, Henan Institute of Science and Technology, Xinxiang 453003, China
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Hong H, Li M, Chen Y, Wang H, Wang J, Guo B, Gao H, Ren H, Yuan M, Han Y, Qiu L. Genome-wide association studies for soybean epicotyl length in two environments using 3VmrMLM. FRONTIERS IN PLANT SCIENCE 2022; 13:1033120. [PMID: 36452100 PMCID: PMC9704727 DOI: 10.3389/fpls.2022.1033120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/04/2022] [Indexed: 06/17/2023]
Abstract
Germination of soybean seed is the imminent vital process after sowing. The status of plumular axis and radicle determine whether soybean seed can emerge normally. Epicotyl, an organ between cotyledons and first functional leaves, is essential for soybean seed germination, seedling growth and early morphogenesis. Epicotyl length (EL) is a quantitative trait controlled by multiple genes/QTLs. Here, the present study analyzes the phenotypic diversity and genetic basis of EL using 951 soybean improved cultivars and landraces from Asia, America, Europe and Africa. 3VmrMLM was used to analyze the associations between EL in 2016 and 2020 and 1,639,846 SNPs for the identification of QTNs and QTN-by-environment interactions (QEIs)".A total of 180 QTNs and QEIs associated with EL were detected. Among them, 74 QTNs (ELS_Q) and 16 QEIs (ELS_QE) were identified to be associated with ELS (epicotyl length of single plant emergence), and 60 QTNs (ELT_Q) and 30 QEIs (ELT_QE) were identified to be associated with ELT (epicotyl length of three seedlings). Based on transcript abundance analysis, GO (Gene Ontology) enrichment and haplotype analysis, ten candidate genes were predicted within nine genic SNPs located in introns, upstream or downstream, which were supposed to be directly or indirectly involved in the process of seed germination and seedling development., Of 10 candidate genes, two of them (Glyma.04G122400 and Glyma.18G183600) could possibly affect epicotyl length elongation. These results indicate the genetic basis of EL and provides a valuable basis for specific functional studies of epicotyl traits.
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Affiliation(s)
- Huilong Hong
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mei Li
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yijie Chen
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Haorang Wang
- Jiangsu Xuhuai Regional Institute of Agricultural Sciences, Xuzhou, China
| | - Jun Wang
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Bingfu Guo
- Nanchang Branch of National Center of Oil crops Improvement, Jiangxi Province Key Laboratory of Oil crops Biology, Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Huawei Gao
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honglei Ren
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Ming Yuan
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Lijuan Qiu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, China
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9
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Lin F, Chhapekar SS, Vieira CC, Da Silva MP, Rojas A, Lee D, Liu N, Pardo EM, Lee YC, Dong Z, Pinheiro JB, Ploper LD, Rupe J, Chen P, Wang D, Nguyen HT. Breeding for disease resistance in soybean: a global perspective. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3773-3872. [PMID: 35790543 PMCID: PMC9729162 DOI: 10.1007/s00122-022-04101-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/11/2022] [Indexed: 05/29/2023]
Abstract
KEY MESSAGE This review provides a comprehensive atlas of QTLs, genes, and alleles conferring resistance to 28 important diseases in all major soybean production regions in the world. Breeding disease-resistant soybean [Glycine max (L.) Merr.] varieties is a common goal for soybean breeding programs to ensure the sustainability and growth of soybean production worldwide. However, due to global climate change, soybean breeders are facing strong challenges to defeat diseases. Marker-assisted selection and genomic selection have been demonstrated to be successful methods in quickly integrating vertical resistance or horizontal resistance into improved soybean varieties, where vertical resistance refers to R genes and major effect QTLs, and horizontal resistance is a combination of major and minor effect genes or QTLs. This review summarized more than 800 resistant loci/alleles and their tightly linked markers for 28 soybean diseases worldwide, caused by nematodes, oomycetes, fungi, bacteria, and viruses. The major breakthroughs in the discovery of disease resistance gene atlas of soybean were also emphasized which include: (1) identification and characterization of vertical resistance genes reside rhg1 and Rhg4 for soybean cyst nematode, and exploration of the underlying regulation mechanisms through copy number variation and (2) map-based cloning and characterization of Rps11 conferring resistance to 80% isolates of Phytophthora sojae across the USA. In this review, we also highlight the validated QTLs in overlapping genomic regions from at least two studies and applied a consistent naming nomenclature for these QTLs. Our review provides a comprehensive summary of important resistant genes/QTLs and can be used as a toolbox for soybean improvement. Finally, the summarized genetic knowledge sheds light on future directions of accelerated soybean breeding and translational genomics studies.
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Affiliation(s)
- Feng Lin
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Sushil Satish Chhapekar
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
| | - Caio Canella Vieira
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Marcos Paulo Da Silva
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Alejandro Rojas
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Dongho Lee
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Nianxi Liu
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun,, 130033 Jilin China
| | - Esteban Mariano Pardo
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA) [Estación Experimental Agroindustrial Obispo Colombres (EEAOC) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)], Av. William Cross 3150, C.P. T4101XAC, Las Talitas, Tucumán, Argentina
| | - Yi-Chen Lee
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Zhimin Dong
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun,, 130033 Jilin China
| | - Jose Baldin Pinheiro
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ/USP), PO Box 9, Piracicaba, SP 13418-900 Brazil
| | - Leonardo Daniel Ploper
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA) [Estación Experimental Agroindustrial Obispo Colombres (EEAOC) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)], Av. William Cross 3150, C.P. T4101XAC, Las Talitas, Tucumán, Argentina
| | - John Rupe
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Pengyin Chen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
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10
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Khan MHU, Wang S, Wang J, Ahmar S, Saeed S, Khan SU, Xu X, Chen H, Bhat JA, Feng X. Applications of Artificial Intelligence in Climate-Resilient Smart-Crop Breeding. Int J Mol Sci 2022; 23:11156. [PMID: 36232455 PMCID: PMC9570104 DOI: 10.3390/ijms231911156] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/18/2022] [Accepted: 09/19/2022] [Indexed: 11/21/2022] Open
Abstract
Recently, Artificial intelligence (AI) has emerged as a revolutionary field, providing a great opportunity in shaping modern crop breeding, and is extensively used indoors for plant science. Advances in crop phenomics, enviromics, together with the other "omics" approaches are paving ways for elucidating the detailed complex biological mechanisms that motivate crop functions in response to environmental trepidations. These "omics" approaches have provided plant researchers with precise tools to evaluate the important agronomic traits for larger-sized germplasm at a reduced time interval in the early growth stages. However, the big data and the complex relationships within impede the understanding of the complex mechanisms behind genes driving the agronomic-trait formations. AI brings huge computational power and many new tools and strategies for future breeding. The present review will encompass how applications of AI technology, utilized for current breeding practice, assist to solve the problem in high-throughput phenotyping and gene functional analysis, and how advances in AI technologies bring new opportunities for future breeding, to make envirotyping data widely utilized in breeding. Furthermore, in the current breeding methods, linking genotype to phenotype remains a massive challenge and impedes the optimal application of high-throughput field phenotyping, genomics, and enviromics. In this review, we elaborate on how AI will be the preferred tool to increase the accuracy in high-throughput crop phenotyping, genotyping, and envirotyping data; moreover, we explore the developing approaches and challenges for multiomics big computing data integration. Therefore, the integration of AI with "omics" tools can allow rapid gene identification and eventually accelerate crop-improvement programs.
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Affiliation(s)
- Muhammad Hafeez Ullah Khan
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- Zhejiang Lab, Hangzhou 310012, China
| | - Shoudong Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- Zhejiang Lab, Hangzhou 310012, China
| | - Jun Wang
- Zhejiang Lab, Hangzhou 310012, China
| | - Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Sumbul Saeed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shahid Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | | | | | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- Zhejiang Lab, Hangzhou 310012, China
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11
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Fallah M, Jean M, Boucher St-Amour VT, O'Donoughue L, Belzile F. The construction of a high-density consensus genetic map for soybean based on SNP markers derived from genotyping-by-sequencing. Genome 2022; 65:413-425. [PMID: 35658547 DOI: 10.1139/gen-2021-0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genetic linkage maps are used to localize markers on the genome based on the recombination frequency. Most often, these maps are based on the segregation observed within a single biparental population of limited size (n < 300) where relatively few recombination events are sampled and in which some genomic regions are monomorphic because both parents carry the same alleles. Together, these two limitations affect both the resolution and extent of genome coverage of such maps. Consensus genetic maps overcome the limitations of individual genetic maps by merging the information from multiple segregating populations derived from a greater diversity of parental combinations, thus increasing the number of recombination events and reducing the number of monomorphic regions. The aim of this study was to construct a high-density consensus genetic map for single nucleotide polymorphism (SNP) markers obtained through a genotyping-by-sequencing (GBS) approach. Individual genetic maps were generated from six F4:5 mapping populations (n = 278-365), totaling 1857 individuals. The six linkage maps were then merged to produce a consensus map comprising a total of 16 311 mapped SNPs that jointly cover 99.5% of the soybean genome with only two gaps larger than 10 cM. Compared to previous soybean consensus maps, it offers a more extensive and uniform coverage.
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Affiliation(s)
- Manel Fallah
- Institut de Biologie Intégrative et des Systèmes (IBIS), Department of Phytology, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Martine Jean
- Institut de Biologie Intégrative et des Systèmes (IBIS), Department of Phytology, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Vincent-Thomas Boucher St-Amour
- Institut de Biologie Intégrative et des Systèmes (IBIS), Department of Phytology, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Louise O'Donoughue
- CÉROM, Centre de recherche sur les grains Inc., Saint-Mathieu-de-Beloeil, QC J3G 0E2, Canada
| | - François Belzile
- Institut de Biologie Intégrative et des Systèmes (IBIS), Department of Phytology, Université Laval, Québec City, QC G1V 0A6, Canada
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12
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Derbyshire MC, Newman TE, Khentry Y, Owolabi Taiwo A. The evolutionary and molecular features of the broad-host-range plant pathogen Sclerotinia sclerotiorum. MOLECULAR PLANT PATHOLOGY 2022; 23:1075-1090. [PMID: 35411696 PMCID: PMC9276942 DOI: 10.1111/mpp.13221] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 03/09/2022] [Accepted: 03/25/2022] [Indexed: 05/21/2023]
Abstract
Sclerotinia sclerotiorum is a pathogenic fungus that infects hundreds of plant species, including many of the world's most important crops. Key features of S. sclerotiorum include its extraordinary host range, preference for dicotyledonous plants, relatively slow evolution, and production of protein effectors that are active in multiple host species. Plant resistance to this pathogen is highly complex, typically involving numerous polymorphisms with infinitesimally small effects, which makes resistance breeding a major challenge. Due to its economic significance, S. sclerotiorum has been subjected to a large amount of molecular and evolutionary research. In this updated pathogen profile, we review the evolutionary and molecular features of S. sclerotiorum and discuss avenues for future research into this important species.
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Affiliation(s)
- Mark C. Derbyshire
- Centre for Crop and Disease ManagementSchool of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Toby E. Newman
- Centre for Crop and Disease ManagementSchool of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Yuphin Khentry
- Centre for Crop and Disease ManagementSchool of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
| | - Akeem Owolabi Taiwo
- Centre for Crop and Disease ManagementSchool of Molecular and Life SciencesCurtin UniversityPerthWestern AustraliaAustralia
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13
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Molecular Breeding to Overcome Biotic Stresses in Soybean: Update. PLANTS 2022; 11:plants11151967. [PMID: 35956444 PMCID: PMC9370206 DOI: 10.3390/plants11151967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/16/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022]
Abstract
Soybean (Glycine max (L.) Merr.) is an important leguminous crop and biotic stresses are a global concern for soybean growers. In recent decades, significant development has been carried outtowards identification of the diseases caused by pathogens, sources of resistance and determination of loci conferring resistance to different diseases on linkage maps of soybean. Host-plant resistance is generally accepted as the bestsolution because of its role in the management of environmental and economic conditions of farmers owing to low input in terms of chemicals. The main objectives of soybean crop improvement are based on the identification of sources of resistance or tolerance against various biotic as well as abiotic stresses and utilization of these sources for further hybridization and transgenic processes for development of new cultivars for stress management. The focus of the present review is to summarize genetic aspects of various diseases caused by pathogens in soybean and molecular breeding research work conducted to date.
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14
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Zhu Y, Thyssen GN, Abdelraheem A, Teng Z, Fang DD, Jenkins JN, McCarty JC, Wedegaertner T, Hake K, Zhang J. A GWAS identified a major QTL for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in a MAGIC population of Upland cotton and a meta-analysis of QTLs for Fusarium wilt resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2297-2312. [PMID: 35577933 DOI: 10.1007/s00122-022-04113-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 04/20/2022] [Indexed: 05/16/2023]
Abstract
A major QTL conferring resistance to Fusarium wilt race 4 in a narrow region of chromosome D02 was identified in a MAGIC population of 550 RILs of Upland cotton. Numerous studies have been conducted to investigate the genetic basis of Fusarium wilt (FW, caused by Fusarium oxysporum f. sp. vasinfectum, FOV) resistance using bi-parental and association mapping populations in cotton. In this study, a multi-parent advanced generation inter-cross (MAGIC) population of 550 recombinant inbred lines (RILs), together with their 11 Upland cotton (Gossypium hirsutum) parents, was used to identify QTLs for FOV race 4 (FOV4) resistance. Among the parents, Acala Ultima, M-240 RNR, and Stoneville 474 were the most resistant, while Deltapine Acala 90, Coker 315, and Stoneville 825 were the most susceptible. Twenty-two MAGIC lines were consistently resistant to FOV4. Through a genome-wide association study (GWAS) based on 473,516 polymorphic SNPs, a major FOV4 resistance QTL within a narrow region on chromosomes D02 was detected, allowing identification of 14 candidate genes. Additionally, a meta-analysis of 133 published FW resistance QTLs showed a D subgenome and individual chromosome bias and no correlation between homeologous chromosome pairs. This study represents the first GWAS study using a largest genetic population and the most comprehensive meta-analysis for FW resistance in cotton. The results illustrated that 550 lines were not enough for high resolution mapping to pinpoint a candidate gene, and experimental errors in phenotyping cotton for FW resistance further compromised the accuracy and precision in QTL localization and identification of candidate genes. This study identified FOV4-resistant parents and MAGIC lines, and the first major QTL for FOV4 resistance in Upland cotton, providing useful information for developing FOV4-resistant cultivars and further genomic studies towards identification of causal genes for FOV4 resistance in cotton.
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Affiliation(s)
- Yi Zhu
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Gregory N Thyssen
- Cotton Fiber Bioscience and Cotton Chemistry and Utilization Research Units, USDA-ARS-SRRC, New Orleans, LA, USA
| | - Abdelraheem Abdelraheem
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Zonghua Teng
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, USA
| | - Johnie N Jenkins
- Crop Science Research Laboratory, USDA-ARS, Mississippi State, MS, USA
| | - Jack C McCarty
- Crop Science Research Laboratory, USDA-ARS, Mississippi State, MS, USA
| | | | | | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
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15
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Sun M, Na C, Jing Y, Cui Z, Li N, Zhan Y, Teng W, Li Y, Li W, Zhao X, Han Y. Genome-Wide Association Analysis and Gene Mining of Resistance to China Race 1 of Frogeye Leaf Spot in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:867713. [PMID: 35812941 PMCID: PMC9257224 DOI: 10.3389/fpls.2022.867713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Soybean frogeye leaf spot (FLS) is a worldwide fungal disease. Its higher occurrence frequency and wider distribution range always led to severe yield losses of soybean, therefore, breeding new cultivars with FLS resistance has been an important breeding goal for soybean breeders. In this study, an association panel of 183 representative soybean accessions was used to evaluate their resistance to FLS race 1, and to identify quantitative trait nucleotides (QTNs) and candidate genes based on genome-wide association study (GWAS) and high-throughput single-nucleotide polymorphisms (SNPs). A total of 23,156 high-quality SNPs were developed using the specific locus-amplified fragment sequencing (SLAF-seq) approach. Finally, 13 novel association signals associated with FLS race 1 resistance were identified by the compressed mixed linear model (CMLM). In addition, 119 candidate genes were found within the 200-kb flanking genomic region of these 13 peak SNPs. Based on the gene-based association analysis, haplotype analysis, expression pattern analysis, and virus-induced gene silencing (VIGS) systems, four genes (Glyma.05G121100, Glyma.17G228300, Glyma.19G006900, and Glyma.19G008700) were preliminarily proved to play an important role in the soybean resistance to FLS race 1.
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Affiliation(s)
- Maolin Sun
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Chen Na
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Yan Jing
- College of Tropical Crops, Hainan University, Haikou, China
| | - Zhihui Cui
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Na Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Yuhang Zhan
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Yongguang Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, China
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16
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Li L, Cui S, Dang P, Yang X, Wei X, Chen K, Liu L, Chen CY. GWAS and bulked segregant analysis reveal the Loci controlling growth habit-related traits in cultivated Peanut (Arachis hypogaea L.). BMC Genomics 2022; 23:403. [PMID: 35624420 PMCID: PMC9145184 DOI: 10.1186/s12864-022-08640-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 05/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background Peanut (Arachis hypogaea L.) is a grain legume crop that originated from South America and is now grown around the world. Peanut growth habit affects the variety’s adaptability, planting patterns, mechanized harvesting, disease resistance, and yield. The objective of this study was to map the quantitative trait locus (QTL) associated with peanut growth habit-related traits by combining the genome-wide association analysis (GWAS) and bulked segregant analysis sequencing (BSA-seq) methods. Results GWAS was performed with 17,223 single nucleotide polymorphisms (SNPs) in 103 accessions of the U.S. mini core collection genotyped using an Affymetrix version 2.0 SNP array. With a total of 12,342 high-quality polymorphic SNPs, the 90 suggestive and significant SNPs associated with lateral branch angle (LBA), main stem height (MSH), lateral branch height (LBL), extent radius (ER), and the index of plant type (IOPT) were identified. These SNPs were distributed among 15 chromosomes. A total of 597 associated candidate genes may have important roles in biological processes, hormone signaling, growth, and development. BSA-seq coupled with specific length amplified fragment sequencing (SLAF-seq) method was used to find the association with LBA, an important trait of the peanut growth habit. A 4.08 Mb genomic region on B05 was associated with LBA. Based on the linkage disequilibrium (LD) decay distance, we narrowed down and confirmed the region within the 160 kb region (144,193,467–144,513,467) on B05. Four candidate genes in this region were involved in plant growth. The expression levels of Araip.E64SW detected by qRT-PCR showed significant difference between ‘Jihua 5’ and ‘M130’. Conclusions In this study, the SNP (AX-147,251,085 and AX-144,353,467) associated with LBA by GWAS was overlapped with the results in BSA-seq through combined analysis of GWAS and BSA-seq. Based on LD decay distance, the genome range related to LBA on B05 was shortened to 144,193,467–144,513,467. Three candidate genes related to F-box family proteins (Araip.E64SW, Araip.YG1LK, and Araip.JJ6RA) and one candidate gene related to PPP family proteins (Araip.YU281) may be involved in plant growth and development in this genome region. The expression analysis revealed that Araip.E64SW was involved in peanut growth habits. These candidate genes will provide molecular targets in marker-assisted selection for peanut growth habits. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08640-3.
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Affiliation(s)
- Li Li
- State Key Laboratory for Crop Improvement and Regulation in North China, College of Agronomy, Hebei Agricultural University, Baoding, 071001, The People's Republic of China.,Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36948, USA.,School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, The People's Republic of China
| | - Shunli Cui
- State Key Laboratory for Crop Improvement and Regulation in North China, College of Agronomy, Hebei Agricultural University, Baoding, 071001, The People's Republic of China
| | - Phat Dang
- USDA-ARS National Peanut Research Laboratory, Dawson, GA, 39842, USA
| | - Xinlei Yang
- State Key Laboratory for Crop Improvement and Regulation in North China, College of Agronomy, Hebei Agricultural University, Baoding, 071001, The People's Republic of China
| | - Xuejun Wei
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, The People's Republic of China
| | - Kai Chen
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, 056038, The People's Republic of China
| | - Lifeng Liu
- State Key Laboratory for Crop Improvement and Regulation in North China, College of Agronomy, Hebei Agricultural University, Baoding, 071001, The People's Republic of China.
| | - Charles Y Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36948, USA.
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17
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Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q, Yang X, Duan Z, Liu Y, Kong F, Liu B, Ren B, Tian Z. Progress in soybean functional genomics over the past decade. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:256-282. [PMID: 34388296 PMCID: PMC8753368 DOI: 10.1111/pbi.13682] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 05/24/2023]
Abstract
Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.
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Affiliation(s)
- Min Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Zhao Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qianjin Liang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Bo Ren
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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Zhang Y, Wang Y, Zhou W, Zheng S, Ye R. Detection of candidate gene networks involved in resistance to Sclerotinia sclerotiorum in soybean. J Appl Genet 2022; 63:1-14. [PMID: 34510383 PMCID: PMC8755693 DOI: 10.1007/s13353-021-00654-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 06/30/2021] [Accepted: 07/17/2021] [Indexed: 11/25/2022]
Abstract
Quantitative trait locus (QTL) mapping often yields associations with dissimilar loci/genes as a consequence of diverse factors. One trait for which very limited agreement between mapping studies has been observed is resistance to white mold in soybean. To explore whether different approaches applied to a single data set could lead to more consistent results, haplotype-trait association and epistasis interaction effects were explored as a complement to a more conventional marker-trait analysis. At least 10 genomic regions were significantly associated with Sclerotinia sclerotiorum resistance in soybean, which have not been previously reported. At a significance level of α = 0.05, haplotype-trait association showed that the most prominent signal originated from a haplotype with 4-SNP (single nucleotide polymorphism) on chromosome 17, and single SNP-trait analysis located a nucleotide polymorphism at position rs34387780 on chromosome 3. All of the peak-SNPs (p-value < 0.05) of each chromosome also appeared in their respective haplotypes. Samples with extreme phenotypes were singled-out for association studies, 25-30% from each end of the phenotypic spectrum appeared in the present investigation to be the most appropriate sample size. Some key genes were identified by epistasis interaction analysis. By combining information on the nearest positional genes indicated that most loci have not been previously reported. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses suggest potential candidate genes underlying callose deposition in the cell wall and mitogen-activated protein kinase (MAPK) signaling pathway-plant, as well as plant-pathogen interaction pathway, were activated. Integration of multi-method genome-wide association study (GWAS) revealed novel genomic regions and promising candidate genes in novel regions, which include Glyma.01g048500, Glyma.03g129100, Glyma.17g072200, and the Dishevelled (Dvl) family of proteins on chromosomes 1, 3, 17, and 20, respectively.
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Affiliation(s)
- Yu Zhang
- School of Biological Sciences and Engineering, Shaanxi University of Technology, Hanzhong, 72300 Shaanxi China
| | - Yuexing Wang
- College of Agronomy, Xinjiang Agricultural University, Urumqi, 830052 China
| | - Wanying Zhou
- School of Biological Sciences and Engineering, Shaanxi University of Technology, Hanzhong, 72300 Shaanxi China
| | - Shimao Zheng
- School of Biological Sciences and Engineering, Shaanxi University of Technology, Hanzhong, 72300 Shaanxi China
| | - Runzhou Ye
- Faculté de Médecine Et Des Sciences de La Santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
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19
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Ferreira EGC, Marcelino-Guimarães FC. Mapping Major Disease Resistance Genes in Soybean by Genome-Wide Association Studies. Methods Mol Biol 2022; 2481:313-340. [PMID: 35641772 DOI: 10.1007/978-1-0716-2237-7_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Soybean is one of the most valuable agricultural crops in the world. Besides, this legume is constantly attacked by a wide range of pathogens (fungi, bacteria, viruses, and nematodes) compromising yield and increasing production costs. One of the major disease management strategies is the genetic resistance provided by single genes and quantitative trait loci (QTL). Identifying the genomic regions underlying the resistance against these pathogens on soybean is one of the first steps performed by molecular breeders. In the past, genetic mapping studies have been widely used to discover these genomic regions. However, over the last decade, advances in next-generation sequencing technologies and their subsequent cost decreasing led to the development of cost-effective approaches to high-throughput genotyping. Thus, genome-wide association studies applying thousands of SNPs in large sets composed of diverse soybean accessions have been successfully done. In this chapter, a comprehensive review of the majority of GWAS for soybean diseases published since this approach was developed is provided. Important diseases caused by Heterodera glycines, Phytophthora sojae, and Sclerotinia sclerotiorum have been the focus of the several GWAS. However, other bacterial and fungi diseases also have been targets of GWAS. As such, this GWAS summary can serve as a guide for future studies of these diseases. The protocol begins by describing several considerations about the pathogens and bringing different procedures of molecular characterization of them. Advice to choose the best isolate/race to maximize the discovery of multiple R genes or to directly map an effective R gene is provided. A summary of protocols, methods, and tools to phenotyping the soybean panel is given to several diseases. We also give details of options of DNA extraction protocols and genotyping methods, and we describe parameters of SNP quality to soybean data. Websites and their online tools to obtain genotypic and phenotypic data for thousands of soybean accessions are highlighted. Finally, we report several tricks and tips in Subheading 4, especially related to composing the soybean panel as well as generating and analyzing the phenotype data. We hope this protocol will be helpful to achieve GWAS success in identifying resistance genes on soybean.
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20
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Mengistu G, Shimelis H, Assefa E, Lule D. Genome-wide association analysis of anthracnose resistance in sorghum [Sorghum bicolor (L.) Moench]. PLoS One 2021; 16:e0261461. [PMID: 34929013 PMCID: PMC8687563 DOI: 10.1371/journal.pone.0261461] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 12/02/2021] [Indexed: 11/18/2022] Open
Abstract
In warm-humid ago-ecologies of the world, sorghum [Sorghum bicolor (L.) Moench] production is severely affected by anthracnose disease caused by Colletotrichum sublineolum Henn. New sources of anthracnose resistance should be identified to introgress novel genes into susceptible varieties in resistance breeding programs. The objective of this study was to determine genome-wide association of Diversity Arrays Technology Sequencing (DArTseq) based single nucleotide polymorphisms (SNP) markers and anthracnose resistance genes in diverse sorghum populations for resistance breeding. Three hundred sixty-six sorghum populations were assessed for anthracnose resistance in three seasons in western Ethiopia using artificial inoculation. Data on anthracnose severity and the relative area under the disease progress curve were computed. Furthermore, the test populations were genotyped using SNP markers with DArTseq protocol. Population structure analysis and genome-wide association mapping were undertaken based on 11,643 SNPs with <10% missing data. The evaluated population was grouped into eight distinct genetic clusters. A total of eight significant (P < 0.001) marker-trait associations (MTAs) were detected, explaining 4.86–15.9% of the phenotypic variation for anthracnose resistance. Out of which the four markers were above the cutoff point. The significant MTAs in the assessed sorghum population are useful for marker-assisted selection (MAS) in anthracnose resistance breeding programs and for gene and quantitative trait loci (QTL) mapping.
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Affiliation(s)
- Girma Mengistu
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
- Oromia Agricultural Research Institute, Addis Ababa, Ethiopia
- * E-mail:
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Ermias Assefa
- Ethiopian Biotechnology Institute, Bioinformatics and Genomics Research Directorate (BGRD), Addis Ababa, Ethiopia
| | - Dagnachew Lule
- Oromia Agricultural Research Institute, Addis Ababa, Ethiopia
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21
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Zhou F, Cui YX, Ma YH, Wang JY, Hu HY, Li SW, Zhang FL, Li CW. Investigating the Potential Mechanism of Pydiflumetofen Resistance in Sclerotinia sclerotiorum. PLANT DISEASE 2021; 105:3580-3585. [PMID: 33934629 DOI: 10.1094/pdis-03-21-0455-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The necrotrophic pathogen Sclerotinia sclerotiorum is one of the most damaging and economically important plant pathogens. Pydiflumetofen, which was developed by Syngenta Crop Protection, has already been registered in China for the management of Sclerotinia stem rot, which was caused by S. sclerotiorum in oilseed rape. In an attempt to preempt and forestall the development of resistance to this useful fungicide, the current study was initiated to investigate the potential mechanism of resistance in laboratory mutants. Five pydiflumetofen-resistant S. sclerotiorum mutants were successfully generated by repeated exposure to the fungicide under laboratory conditions. Although the mutants had greatly reduced sensitivity to pydiflumetofen, they were also found to have significantly (P < 0.05) reduced fitness, exhibiting reduced mycelial growth and sclerotia formation on potato dextrose agar medium. However, three of the four mutants had significantly (P < 0.05) increased pathogenicity on detached soybean leaves compared with their respective parental isolates, indicating a moderate to high level of fungicide resistance risk according to the criteria of the Fungicide Resistance Action Committee. Sequence analysis of four succinate dehydrogenase (Sdh) target genes identified several nucleotide changes in the sequences of the pydiflumetofen-resistant mutants, most of which were synonymous and caused no changes to the predicted amino acid sequences. However, all of the pydiflumetofen-resistant mutants had two amino acid point mutations (A11V and V162A) in their predicted SsSdhB sequence. No similar changes were found in the SsSdhA, SsSdhC, and SsSdhD genes of any of the mutants tested. In addition, there was a positive cross-resistance between pydiflumetofen and boscalid, and no cross-resistance between pydiflumetofen and other commonly used fungicides, including tebuconazole, fludioxonil, cyprodinil, dimethachlone, prochloraz, pyraclostrobin, fluazinam, procymidone, and carbendazim. These results indicate that pydiflumetofen has great potential as an alternative fungicide for the control of S. sclerotiorum, especially where resistance to other fungicides has already emerged. Mixing or alternate application with fludioxonil, prochloraz, and fluazinam could be used to limit the risk of resistance to pydiflumetofen.
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Affiliation(s)
- F Zhou
- Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Y X Cui
- Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Y H Ma
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - J Y Wang
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - H Y Hu
- Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - S W Li
- Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - F L Zhang
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - C-W Li
- Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
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22
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Li X, Zhou Y, Bu Y, Wang X, Zhang Y, Guo N, Zhao J, Xing H. Genome-wide association analysis for yield-related traits at the R6 stage in a Chinese soybean mini core collection. Genes Genomics 2021; 43:897-912. [PMID: 33956328 DOI: 10.1007/s13258-021-01109-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/26/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND Soybean (Glycine max (L.) Merr.) is an economically important crop for vegetable oil and protein production, and yield is a critical trait for grain/vegetable uses of soybean. However, our knowledge of the genes controlling the vegetable soybean yield remains limited. OBJECTIVE To better understand the genetic basis of the vegetable soybean yield. METHODS The 100-pod fresh weight (PFW), 100-seed fresh weight (SFW), kernel percent (KP) and moisture content of fresh seeds (MCFS) at the R6 stage are four yield-related traits for vegetable soybean. We investigated a soybean mini core collection composed of 224 germplasm accessions for four yield-related traits in two consecutive years. Based on 1514 single nucleotide polymorphisms (SNPs), genome-wide association studies (GWAS) were conducted using a mixed linear model (MLM). RESULTS Extensive phenotypic variation existed in the soybean mini core collection and significant positive correlations were shown among most of traits. A total of 16 SNP markers for PFW, SFW, KP and MCFS were detected in all environments via GWAS. Nine SNP markers were repeatedly identified in two environments. Among these markers, eight were located in or near regions where yield-related QTLs have been reported in previous studies, and one was a novel genetic locus identified in this study. In addition, we conducted candidate gene analysis to the large-effect SNP markers, a total of twelve genes were proposed as potential candidate genes of soybean yield at the R6 stage. CONCLUSION These results will be beneficial for understanding the genetic basis of soybean yield at the R6 stage and facilitating the pyramiding of favourable alleles for future high-yield breeding by marker-assisted selection in vegetable soybean.
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Affiliation(s)
- Xiangnan Li
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Yang Zhou
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Yuanpeng Bu
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Xinfang Wang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Yumei Zhang
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Na Guo
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China
| | - Jinming Zhao
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China.
| | - Han Xing
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Weigang No. 1, Nanjing, 210095, Jiangsu, China.
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23
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Jianan Z, Li W, Zhang Y, Song W, Jiang H, Zhao J, Zhan Y, Teng W, Qiu L, Zhao X, Han Y. Identification of glutathione transferase gene associated with partial resistance to Sclerotinia stem rot of soybean using genome-wide association and linkage mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2699-2709. [PMID: 34057551 DOI: 10.1007/s00122-021-03855-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE Association and linkage mapping techniques were used to identify and verify single nucleotide polymorphisms (SNPs) associated with Sclerotinia sclerotiorum resistance. A novel resistant gene, GmGST , was cloned and shown to be involved in soybean resistance to SSR. Sclerotinia stem rot (SSR), caused by the fungus Sclerotinia sclerotiorum, is one of the most devastating diseases in soybean (Glycine max (Linn.) Merr.) However, the genetic architecture underlying soybean resistance to SSR is poorly understood, despite several mapping and gene mining studies. In the present study, the identification of quantitative trait loci (QTLs) involved in the resistance to S. sclerotiorum was conducted in two segregating populations: an association population that consisted of 261 diverse soybean germplasms, and the MH population, derived from a cross between a partially resistant cultivar (Maple arrow) and a susceptible cultivar (Hefeng25). Three and five genomic regions affecting resistance were detected by genome-wide association study to control the lesion length of stems (LLS) and the death rate of seedling (DRS), respectively. Four QTLs were detected to underlie LLS, and one QTL controlled DRS after SSR infection. A major locus on chromosome (Chr.) 13 (qDRS13-1), which affected both DRS and LLS, was detected in both the natural population and the MH population. GmGST, encoding a glutathione S-transferase, was cloned as a candidate gene in qDRS13-1. GmGST was upregulated by the induction of the partially resistant cultivar Maple arrow. Transgenic experiments showed that the overexpression of GmGST in soybean increased resistance to S. sclerotiorum and the content of soluble pigment in stems of soybean. The results increase our understanding of the genetic architecture of soybean resistance to SSR and provide a framework for the future marker-assisted breeding of resistant soybean cultivars.
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Affiliation(s)
- Zou Jianan
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Wenjing Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Yuting Zhang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Wei Song
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Haipeng Jiang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Jingyun Zhao
- Zhumadian Academy of Agricultural Sciences, Zhumadian, 463000, China
| | - Yuhang Zhan
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, 150030, China
| | - Lijuan Qiu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, 150030, China.
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry, Northeast Agricultural University, Harbin, 150030, China.
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24
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Zhou F, Hu HY, Li DX, Tan LG, Zhang Q, Gao HT, Sun HL, Tian XL, Shi MW, Zhang FL, Li CW. Exploring the Biological and Molecular Characteristics of Resistance to Fludioxonil in Sclerotinia sclerotiorum From Soybean in China. PLANT DISEASE 2021; 105:1936-1941. [PMID: 33044139 DOI: 10.1094/pdis-07-20-1621-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Sclerotinia sclerotiorum is one of the most damaging and economically important necrotrophic plant pathogens, infecting more than 400 plant species globally. Although the phenylpyrrole fungicide fludioxonil has high activity against S. sclerotiorum, reports indicate that there is also substantial potential for the development of fungicide resistance. However, the current study investigating five fludioxonil-resistant laboratory mutants found a significant fitness cost associated with fludioxonil resistance resulting in significantly (P < 0.05) reduced mycelial growth and sclerotia formation on potato dextrose agar as well as significantly (P < 0.05) lower pathogenicity on detached tomato leaves, with one mutant, LK-1R, completely losing the capacity to cause infection. In addition, all of the fludioxonil-resistant mutants had significantly (P < 0.05) increased sensitivity to osmotic stress (0.5 M of potassium chloride and 1.0 M of glucose), which is consistent with the proposed fludioxonil target sites within the high osmolarity glycerol stress response mitogen-activated protein kinase (HOG1-MAPK) signaling transduction pathway. Sequence analysis of six genes from this two-component pathway, including SsHk, SsYpd, SsSk1, SsSk2, SsPbs, and SsHog, revealed several mutations that may be associated with fludioxonil resistance. For example, six separate point mutations were found in SsHk that led to changes in the predicted amino acid sequence, including A136G, F249V, G353A, E560K, M610K, and K727R. Similarly, SsPbs had three mutations (D34G, S46L, and L337E), SsSk1 and SsYpd had two (S53G and A795V for SsSk1, and E67G and Y141H for SsYpd), and SsHog and SsSk2 had one each (V220A and S763P, respectively). To our knowledge, these constitute the first reports of amino acid changes in proteins of the HOG1-MAPK pathway being associated with fludioxonil resistance in S. sclerotiorum. This study also showed a positive cross-resistance between fludioxonil and dimethachlone and procymidone, but none with tebuconazole or carbendazim, indicating that the inclusion of tebuconazole within an integrated pest management program could reduce the risk of fludioxonil resistance developing in field populations of S. sclerotiorum and ensure the sustainable production of soybeans in China into the future.
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Affiliation(s)
- F Zhou
- Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
- Henan Engineering Research Center of Biological Pesticide and Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - H Y Hu
- Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - D X Li
- Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - L G Tan
- Henan Engineering Research Center of Biological Pesticide and Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Q Zhang
- Henan Engineering Research Center of Biological Pesticide and Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - H T Gao
- Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - H L Sun
- Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - X L Tian
- Henan Engineering Research Center of Biological Pesticide and Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - M W Shi
- Henan Engineering Research Center of Biological Pesticide and Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - F L Zhang
- Henan Engineering Research Center of Biological Pesticide and Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - C W Li
- Henan Engineering Research Center of Crop Genome Editing, Henan Institute of Science and Technology, Xinxiang 453003, China
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Genome-wide association studies: assessing trait characteristics in model and crop plants. Cell Mol Life Sci 2021; 78:5743-5754. [PMID: 34196733 PMCID: PMC8316211 DOI: 10.1007/s00018-021-03868-w] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 01/19/2023]
Abstract
GWAS involves testing genetic variants across the genomes of many individuals of a population to identify genotype–phenotype association. It was initially developed and has proven highly successful in human disease genetics. In plants genome-wide association studies (GWAS) initially focused on single feature polymorphism and recombination and linkage disequilibrium but has now been embraced by a plethora of different disciplines with several thousand studies being published in model and crop species within the last decade or so. Here we will provide a comprehensive review of these studies providing cases studies on biotic resistance, abiotic tolerance, yield associated traits, and metabolic composition. We also detail current strategies of candidate gene validation as well as the functional study of haplotypes. Furthermore, we provide a critical evaluation of the GWAS strategy and its alternatives as well as future perspectives that are emerging with the emergence of pan-genomic datasets.
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Jing Y, Teng W, Qiu L, Zheng H, Li W, Han Y, Zhao X. Genetic dissection of soybean partial resistance to sclerotinia stem rot through genome wide association study and high throughout single nucleotide polymorphisms. Genomics 2021; 113:1262-1271. [PMID: 33689785 DOI: 10.1016/j.ygeno.2020.10.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/08/2020] [Accepted: 10/30/2020] [Indexed: 10/22/2022]
Abstract
Sclerotinia stem rot (SSR) is a disease of soybean [Glycine max (L.) Merr] that causes severe yield losses. We studied 185 representative soybean accessions to evaluate partial SSR resistance and sequenced these by the specific-locus amplified fragment sequencing method. In total, 22,048 single-nucleotide polymorphisms (SNPs), with minor allele frequencies (MAF) ≥5% and missing data <3%, were developed and applied to genome-wide association study of SSR responsiveness and assess linkage disequilibrium (LD) level for candidate gene selection. We identified 18 association signals related to SSR partial resistance. Among them, six overlapped the regions of previous quantitative trait loci, and twelve were novel. We identified 243 candidate genes located in the 200 kb genomic region of these peak SNPs. Based on quantitative real-time polymerase chain reaction and haplotype analysis, Glyma.03G196000 and Glyma.20G095100, encoding pentatricopeptide repeat proteins, might be important factors in the resistance response of soybean to SSR.
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Affiliation(s)
- Yan Jing
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, 150030. Harbin, China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, 150030. Harbin, China
| | - Lijuan Qiu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Hongkun Zheng
- Bioinformatics Division, Biomarker Technologies Corporation, 101300, Beijing, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, 150030. Harbin, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, 150030. Harbin, China.
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, 150030. Harbin, China.
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Sun M, Jing Y, Zhao X, Teng W, Qiu L, Zheng H, Li W, Han Y. Genome-wide association study of partial resistance to sclerotinia stem rot of cultivated soybean based on the detached leaf method. PLoS One 2020; 15:e0233366. [PMID: 32421759 PMCID: PMC7233537 DOI: 10.1371/journal.pone.0233366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
Sclerotinia stem rot (SSR) is a devastating fungal disease that causes severe yield losses of soybean worldwide. In the present study, a representative population of 185 soybean accessions was selected and utilized to identify the quantitative trait nucleotide (QTN) of partial resistance to soybean SSR via a genome-wide association study (GWAS). A total of 22,048 single-nucleotide polymorphisms (SNPs) with minor allele frequencies (MAF) > 5% and missing data < 3% were used to assess linkage disequilibrium (LD) levels. Association signals associated with SSR partial resistance were identified by two models, including compressed mixed linear model (CMLM) and multi-locus random-SNP-effect mixed linear model (mrMLM). Finally, seven QTNs with major effects (a known locus and six novel loci) via CMLM and nine novel QTNs with minor effects via mrMLM were detected in relation to partial resistance to SSR, respectively. One of all the novel loci (Gm05:14834789 on Chr.05), which was co-located by these two methods, might be a stable one that showed high significance in SSR partial resistance. Additionally, a total of 71 major and 85 minor candidate genes located in the 200-kb genomic region of each peak SNP detected by CMLM and mrMLM were found, respectively. By using a gene-based association, a total of six SNPs from three major effects genes and eight SNPs from four minor effects genes were identified. Of them, Glyma.18G012200 has been characterized as a significant element in controlling fungal disease in plants.
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Affiliation(s)
- Mingming Sun
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
- Heilongjiang Journal Press of Agricultural Science and Technology, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yan Jing
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Lijuan Qiu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongkun Zheng
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
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Boudhrioua C, Bastien M, Torkamaneh D, Belzile F. Genome-wide association mapping of Sclerotinia sclerotiorum resistance in soybean using whole-genome resequencing data. BMC PLANT BIOLOGY 2020; 20:195. [PMID: 32380949 PMCID: PMC7333386 DOI: 10.1186/s12870-020-02401-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 04/21/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. RESULTS In this study, we identified a major quantitative trait loci (QTL) associated with resistance to SSR progression on the main stem by using a genome-wide association mapping (GWAM). A population of 127 soybean accessions was genotyped with 1.5 M SNPs derived from genotyping-by-sequencing (GBS) and whole-genome sequencing (WGS) ensuring an extensive genome coverage and phenotyped for SSR resistance. SNP-trait association led to discovery of a new QTL on chromosome 1 (Chr01) where resistant lines had shorter lesions on the stem by 29 mm. A single gene (Glyma.01 g048000) resided in the same LD block as the peak SNP, but it is of unknown function. The impact of this QTL was even more significant in the descendants of a cross between two lines carrying contrasted alleles for Chr01. Individuals carrying the resistance allele developed lesions almost 50% shorter than those bearing the sensitivity allele. CONCLUSION These results suggest that the new region on chromosome 1 harbors a promising resistance QTL to SSR that can be used in soybean breeding program.
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Affiliation(s)
- Chiheb Boudhrioua
- Département de phytologie and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, G1V0A6, Canada
| | - Maxime Bastien
- Département de phytologie and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, G1V0A6, Canada
| | - Davoud Torkamaneh
- Département de phytologie and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, G1V0A6, Canada
| | - François Belzile
- Département de phytologie and Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, G1V0A6, Canada.
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Fang H, Liu H, Ma R, Liu Y, Li J, Yu X, Zhang H, Yang Y, Zhang G. Genome-wide assessment of population structure and genetic diversity of Chinese Lou onion using specific length amplified fragment (SLAF) sequencing. PLoS One 2020; 15:e0231753. [PMID: 32369481 PMCID: PMC7199963 DOI: 10.1371/journal.pone.0231753] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 03/30/2020] [Indexed: 11/24/2022] Open
Abstract
Lou onion (Allium fistulosum L. var. viviparum) is an abundant source of flavonols which provides additional health benefits to diseases. Genome-wide specific length amplified fragment (SLAF) sequencing method is a rapidly developed deep sequencing technologies used for selection and identification of genetic loci or markers. This study aimed to elucidate the genetic diversity of 122 onion accessions in China using the SLAF-seq method. A set of 122 onion accessions including 107 A.fistulosum L. var. viviparum Makino, 3 A.fistulosum L. var. gigantum Makino, 3 A.mongolicum Regel and 9 A.cepa L. accessions (3 whites, 3 reds and 3 yellows) from different regions in China were enrolled. Genomic DNA was isolated from young leaves and prepared for the SLAF-seq, which generated a total of 1,387.55 M reads and 162,321 high quality SNPs (integrity >0.5 and MAF >0.05). These SNPs were used for the construction of neighbor-joining phylogenetic tree, in which 10 A.fistulosum L. var. viviparum Makino accessions from Yinchuan (Ningxia province) and Datong (Qinghai province) had close genetic relationship. The 3 A.cepa L. clusters (red, white and yellow) had close genetic relationship especially with the 97 A.fistulosum L. var. viviparum Makino accessions. Population structure analysis suggested entire population could be clustered into 3 groups, while principal component analysis (PCA) showed there were 4 genetic groups. We confirmed the SLAF-seq approach was effective in genetic diversity analysis in red onion accessions. The key findings would provide a reference to the Lou onion germplasm in China.
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Affiliation(s)
- Haitian Fang
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
- * E-mail: (HF); (GZ)
| | - Huiyan Liu
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
| | - Ruoshuang Ma
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
| | - Yuxuan Liu
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
| | - Jinna Li
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
| | - Xiaoyan Yu
- Technological Innovation Center of Protected Horticulture (Ningxia University) in Ningxia, Yinchuan, China
- Technological Innovation center of Horticulture (Ningxia University), Ningxia Hui Autonomous Region, Yinchuan, China
| | - Haoyu Zhang
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
| | - Yali Yang
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
| | - Guangdi Zhang
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
- Technological Innovation Center of Protected Horticulture (Ningxia University) in Ningxia, Yinchuan, China
- Technological Innovation center of Horticulture (Ningxia University), Ningxia Hui Autonomous Region, Yinchuan, China
- * E-mail: (HF); (GZ)
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Jiang B, Cheng Y, Cai Z, Li M, Jiang Z, Ma R, Yuan Y, Xia Q, Nian H. Fine mapping of a Phytophthora-resistance locus RpsGZ in soybean using genotyping-by-sequencing. BMC Genomics 2020; 21:280. [PMID: 32245402 PMCID: PMC7126358 DOI: 10.1186/s12864-020-6668-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/12/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Phytophthora root rot (PRR) caused by Phytophthora sojae (P. sojae) is one of the most serious limitations to soybean production worldwide. The identification of resistance gene(s) and their incorporation into elite varieties is an effective approach for breeding to prevent soybean from being harmed by this disease. A valuable mapping population of 228 F8:11 recombinant inbred lines (RILs) derived from a cross of the resistant cultivar Guizao1 and the susceptible cultivar BRSMG68 and a high-density genetic linkage map with an average distance of 0.81 centimorgans (cM) between adjacent bin markers in this population were used to map and explore candidate gene(s). RESULTS PRR resistance in Guizao1 was found to be controlled by a single Mendelian locus and was finely mapped to a 367.371-kb genomic region on chromosome 3 harbouring 19 genes, including 7 disease resistance (R)-like genes, in the reference Willliams 82 genome. Quantitative real-time PCR assays of possible candidate genes revealed that Glyma.03 g05300 was likely involved in PRR resistance. CONCLUSIONS These findings from the fine mapping of a novel Rps locus will serve as a basis for the cloning and transfer of resistance genes in soybean and the breeding of P. sojae-resistant soybean cultivars through marker-assisted selection.
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Affiliation(s)
- Bingzhi Jiang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- Guangdong Provincial Key Laboratory of Crops Genetics and Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 People’s Republic of China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
| | - Mu Li
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
| | - Ze Jiang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
| | - Ruirui Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
| | - Yeshan Yuan
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
| | - Qiuju Xia
- Beijing Genomics Institute (BGI) Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083 People’s Republic of China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642 People’s Republic of China
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Yang X, Yang J, Li H, Niu L, Xing G, Zhang Y, Xu W, Zhao Q, Li Q, Dong Y. Overexpression of the chitinase gene CmCH1 from Coniothyrium minitans renders enhanced resistance to Sclerotinia sclerotiorum in soybean. Transgenic Res 2020; 29:187-198. [PMID: 31970612 DOI: 10.1007/s11248-020-00190-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/09/2020] [Indexed: 10/25/2022]
Abstract
Pathogenic fungi represent one of the major biotic stresses for soybean production across the world. Sclerotinia sclerotiorum, the causal agent of Sclerotinia stem rot, is a devastating fungal pathogen that is responsible for significant yield losses in soybean. In this study, the chitinase gene CmCH1, from the mycoparasitic fungus Coniothyrium minitans, which infects a range of ascomycetous sclerotia, including S. sclerotiorum and S. minor, was introduced into soybean. Transgenic plants expressing CmCH1 showed higher resistance to S. sclerotiorum infection, with significantly reduced lesion sizes in both detached stem and leaf assays, compared to the non-transformed control. Increased hydrogen peroxide content and activities of defense-responsive enzymes, such as peroxidase, superoxide dismutase, phenylalanine ammonia lyase, and polyphenoloxidase were also observed at the infection sites in the transgenic plants inoculated with S. sclerotiorum. Consistent with the role of chitinases in inducing downstream defense responses by the release of elicitors, several defense-related genes, such as GmNPR2, GmSGT-1, GmRAR1, GmPR1, GmPR3, GmPR12, GmPAL, GmAOS, GmPPO, were also significantly upregulated in the CmCH1-expressing soybean after inoculation. Collectively, our results demonstrate that overexpression of CmCH1 led to increased accumulation of H2O2 and up-regulation of defense-related genes and enzymes, and thus enhanced resistance to S. sclerotiorum infection while showing no detrimental effects on growth and development of soybean plants.
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Affiliation(s)
- Xiangdong Yang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Jing Yang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Haiyun Li
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Lu Niu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Guojie Xing
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Yuanyu Zhang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Wenjing Xu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Qianqian Zhao
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Qiyun Li
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| | - Yingshan Dong
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
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Luo Z, Cui R, Chavarro C, Tseng YC, Zhou H, Peng Z, Chu Y, Yang X, Lopez Y, Tillman B, Dufault N, Brenneman T, Isleib TG, Holbrook C, Ozias-Akins P, Wang J. Mapping quantitative trait loci (QTLs) and estimating the epistasis controlling stem rot resistance in cultivated peanut (Arachis hypogaea). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1201-1212. [PMID: 31974667 DOI: 10.1007/s00122-020-03542-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 01/10/2020] [Indexed: 06/10/2023]
Abstract
A total of 33 additive stem rot QTLs were identified in peanut genome with nine of them consistently detected in multiple years or locations. And 12 pairs of epistatic QTLs were firstly reported for peanut stem rot disease. Stem rot in peanut (Arachis hypogaea) is caused by the Sclerotium rolfsii and can result in great economic loss during production. In this study, a recombinant inbred line population from the cross between NC 3033 (stem rot resistant) and Tifrunner (stem rot susceptible) that consists of 156 lines was genotyped by using 58 K peanut single nucleotide polymorphism (SNP) array and phenotyped for stem rot resistance at multiple locations and in multiple years. A linkage map consisting of 1451 SNPs and 73 simple sequence repeat (SSR) markers was constructed. A total of 33 additive quantitative trait loci (QTLs) for stem rot resistance were detected, and six of them with phenotypic variance explained of over 10% (qSR.A01-2, qSR.A01-5, qSR.A05/B05-1, qSR.A05/B05-2, qSR.A07/B07-1 and qSR.B05-1) can be consistently detected in multiple years or locations. Besides, 12 pairs of QTLs with epistatic (additive × additive) interaction were identified. An additive QTL qSR.A01-2 also with an epistatic effect interacted with a novel locus qSR.B07_1-1 to affect the percentage of asymptomatic plants in a row. A total of 193 candidate genes within 38 stem rot QTLs intervals were annotated with functions of biotic stress resistance such as chitinase, ethylene-responsive transcription factors and pathogenesis-related proteins. The identified stem rot resistance QTLs, candidate genes, along with the associated SNP markers in this study, will benefit peanut molecular breeding programs for improving stem rot resistance.
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Affiliation(s)
- Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Renjie Cui
- Department of Plant Pathology, University of Georgia, Tifton, GA, USA
| | - Carolina Chavarro
- Center for Applied Genetic Technologies, Institute of Plant Breeding, Genetics and Genomics, The University of Georgia, Athens, GA, USA
| | - Yu-Chien Tseng
- Agronomy Department, University of Florida, Gainesville, FL, USA
- Department of Agronomy, National Chiayi University, Chiayi, Taiwan
| | - Hai Zhou
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Ye Chu
- Department of Horticulture, Institute for Plant Breeding, Genetics and Genomics, University of Georgia Tifton Campus, Tifton, GA, USA
| | - Xiping Yang
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Yolanda Lopez
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Barry Tillman
- Agronomy Department, University of Florida, Gainesville, FL, USA
- North Florida Research and Education Center, Marianna, FL, USA
| | - Nicholas Dufault
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Timothy Brenneman
- Department of Plant Pathology, University of Georgia, Tifton, GA, USA
| | - Thomas G Isleib
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA
| | - Corley Holbrook
- Crop Genetics and Breeding Research Unit, USDA-ARS, Tifton, GA, USA
| | - Peggy Ozias-Akins
- Department of Horticulture, Institute for Plant Breeding, Genetics and Genomics, University of Georgia Tifton Campus, Tifton, GA, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA.
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Ma Y, Marzougui A, Coyne CJ, Sankaran S, Main D, Porter LD, Mugabe D, Smitchger JA, Zhang C, Amin MN, Rasheed N, Ficklin SP, McGee RJ. Dissecting the Genetic Architecture of Aphanomyces Root Rot Resistance in Lentil by QTL Mapping and Genome-Wide Association Study. Int J Mol Sci 2020; 21:ijms21062129. [PMID: 32244875 PMCID: PMC7139309 DOI: 10.3390/ijms21062129] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 12/15/2022] Open
Abstract
Lentil (Lens culinaris Medikus) is an important source of protein for people in developing countries. Aphanomyces root rot (ARR) has emerged as one of the most devastating diseases affecting lentil production. In this study, we applied two complementary quantitative trait loci (QTL) analysis approaches to unravel the genetic architecture underlying this complex trait. A recombinant inbred line (RIL) population and an association mapping population were genotyped using genotyping by sequencing (GBS) to discover novel single nucleotide polymorphisms (SNPs). QTL mapping identified 19 QTL associated with ARR resistance, while association mapping detected 38 QTL and highlighted accumulation of favorable haplotypes in most of the resistant accessions. Seven QTL clusters were discovered on six chromosomes, and 15 putative genes were identified within the QTL clusters. To validate QTL mapping and genome-wide association study (GWAS) results, expression analysis of five selected genes was conducted on partially resistant and susceptible accessions. Three of the genes were differentially expressed at early stages of infection, two of which may be associated with ARR resistance. Our findings provide valuable insight into the genetic control of ARR, and genetic and genomic resources developed here can be used to accelerate development of lentil cultivars with high levels of partial resistance to ARR.
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Affiliation(s)
- Yu Ma
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (Y.M.); (D.M.); (S.P.F.)
| | - Afef Marzougui
- Department of Biological Systems Engineering, Washington State University, Pullman, WA 99164, USA; (A.M.); (S.S.); (C.Z.)
| | - Clarice J. Coyne
- USDA-ARS Plant Germplasm Introduction and Testing Unit, Washington State University, Pullman, WA 99164, USA;
| | - Sindhuja Sankaran
- Department of Biological Systems Engineering, Washington State University, Pullman, WA 99164, USA; (A.M.); (S.S.); (C.Z.)
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (Y.M.); (D.M.); (S.P.F.)
| | - Lyndon D. Porter
- USDA-ARS Grain Legume Genetics and Physiology Research Unit, Prosser, WA 99350, USA;
| | - Deus Mugabe
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA; (D.M.); (J.A.S.)
| | - Jamin A. Smitchger
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA; (D.M.); (J.A.S.)
| | - Chongyuan Zhang
- Department of Biological Systems Engineering, Washington State University, Pullman, WA 99164, USA; (A.M.); (S.S.); (C.Z.)
| | - Md. Nurul Amin
- Breeder Seed Production Center, Bangladesh Agricultural Research Institute, Debiganj-5020, Panchagarh, Bangladesh;
| | - Naser Rasheed
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad 38000, Pakistan;
| | - Stephen P. Ficklin
- Department of Horticulture, Washington State University, Pullman, WA 99164, USA; (Y.M.); (D.M.); (S.P.F.)
| | - Rebecca J. McGee
- USDA-ARS Grain Legume Genetics and Physiology Research Unit, Pullman, WA 99164, USA
- Correspondence: ; Tel.: +1-509-335-0300
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Wang Z, Zhao FY, Tang MQ, Chen T, Bao LL, Cao J, Li YL, Yang YH, Zhu KM, Liu S, Tan XL. BnaMPK6 is a determinant of quantitative disease resistance against Sclerotinia sclerotiorum in oilseed rape. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110362. [PMID: 31928657 DOI: 10.1016/j.plantsci.2019.110362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 11/04/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Sclerotinia sclerotiorum causes a devastating disease in oilseed rape (Brassica napus), resulting in major economic losses. Resistance response of B. napus against S. sclerotiorum exhibits a typical quantitative disease resistance (QDR) characteristic, but the molecular determinants of this QDR are largely unknown. In this study, we isolated a B. napus mitogen-activated protein kinase gene, BnaMPK6, and found that BnaMPK6 expression is highly responsive to infection by S. sclerotiorum and treatment with salicylic acid (SA) or jasmonic acid (JA). Moreover, overexpression (OE) of BnaMPK6 significantly enhances resistance to S. sclerotiorum, whereas RNAi in BnaMPK6 significantly reduces this resistance. These results showed that BnaMPK6 plays an important role in defense to S. sclerotiorum. Furthermore, expression of defense genes associated with SA-, JA- and ethylene (ET)-mediated signaling was investigated in BnaMPK6-RNAi, WT and BnaMPK6-OE plants after S. sclerotiorum infection, and consequently, it was indicated that the activation of ET signaling by BnaMPK6 may play a role in the defense. Further, four BnaMPK6-encoding homologous loci were mapped in the B. napus genome. Using the allele analysis and expression analysis on the four loci, we demonstrated that the locus BnaA03.MPK6 makes an important contribution to QDR against S. sclerotiorum. Our data indicated that BnaMPK6 is a previously unknown determinant of QDR against S. sclerotiorum in B. napus.
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Affiliation(s)
- Zheng Wang
- Institute of Life Sciences, Jiangsu University, 301#Xuefu Road, Zhenjiang, 212013, PR China
| | - Feng-Yun Zhao
- Institute of Life Sciences, Jiangsu University, 301#Xuefu Road, Zhenjiang, 212013, PR China
| | - Min-Qiang Tang
- The Oil Crops Research Institute (OCRI) of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Ting Chen
- Institute of Life Sciences, Jiangsu University, 301#Xuefu Road, Zhenjiang, 212013, PR China
| | - Ling-Li Bao
- Institute of Life Sciences, Jiangsu University, 301#Xuefu Road, Zhenjiang, 212013, PR China
| | - Jun Cao
- Institute of Life Sciences, Jiangsu University, 301#Xuefu Road, Zhenjiang, 212013, PR China
| | - Yu-Long Li
- Institute of Life Sciences, Jiangsu University, 301#Xuefu Road, Zhenjiang, 212013, PR China
| | - Yan-Hua Yang
- Institute of Life Sciences, Jiangsu University, 301#Xuefu Road, Zhenjiang, 212013, PR China
| | - Ke-Ming Zhu
- Institute of Life Sciences, Jiangsu University, 301#Xuefu Road, Zhenjiang, 212013, PR China
| | - Shengyi Liu
- The Oil Crops Research Institute (OCRI) of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China.
| | - Xiao-Li Tan
- Institute of Life Sciences, Jiangsu University, 301#Xuefu Road, Zhenjiang, 212013, PR China.
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Du H, Zhang H, Wei L, Li C, Duan Y, Wang H. A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.). BMC PLANT BIOLOGY 2019; 19:588. [PMID: 31881840 PMCID: PMC6935206 DOI: 10.1186/s12870-019-2172-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/28/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F2 population by using specific length amplified fragment (SLAF) technique and determined the quantitative trait loci (QTLs) of seed-related traits for sesame based on the phenotypes of F3 progeny. RESULTS The genetic map comprised 2159 SNP markers distributed on 13 linkage groups (LGs) and was 2128.51 cM in length, with an average distance of 0.99 cM between adjacent markers. QTL mapping revealed 19 major-effect QTLs with the phenotypic effect (R2) more than 10%, i.e., eight QTLs for seed coat color, nine QTLs for seed size, and two QTLs for 1000-seed weight (TSW), using composite interval mapping method. Particularly, LG04 and LG11 contained collocated QTL regions for the seed coat color and seed size traits, respectively, based on their close or identical locations. In total, 155 candidate genes for seed coat color, 22 for seed size traits, and 54 for TSW were screened and analyzed. CONCLUSIONS This report presents the first QTL mapping of seed-related traits in sesame using an F2 population. The results reveal the location of specific markers associated with seed-related traits in sesame and provide the basis for further seed quality traits research.
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Affiliation(s)
- Hua Du
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Huili Wang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
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Li M, Liu Y, Tao Y, Xu C, Li X, Zhang X, Han Y, Yang X, Sun J, Li W, Li D, Zhao X, Zhao L. Identification of genetic loci and candidate genes related to soybean flowering through genome wide association study. BMC Genomics 2019; 20:987. [PMID: 31842754 PMCID: PMC6916438 DOI: 10.1186/s12864-019-6324-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/22/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND As a photoperiod-sensitive and self-pollinated species, the growth periods traits play important roles in the adaptability and yield of soybean. To examine the genetic architecture of soybean growth periods, we performed a genome-wide association study (GWAS) using a panel of 278 soybean accessions and 34,710 single nucleotide polymorphisms (SNPs) with minor allele frequencies (MAF) higher than 0.04 detected by the specific-locus amplified fragment sequencing (SLAF-seq) with a 6.14-fold average sequencing depth. GWAS was conducted by a compressed mixed linear model (CMLM) involving in both relative kinship and population structure. RESULTS GWAS revealed that 37 significant SNP peaks associated with soybean flowering time or other growth periods related traits including full bloom, beginning pod, full pod, beginning seed, and full seed in two or more environments at -log10(P) > 3.75 or -log10(P) > 4.44 were distributed on 14 chromosomes, including chromosome 1, 2, 3, 5, 6, 9, 11, 12, 13, 14, 15, 17, 18, 19. Fourteen SNPs were novel loci and 23 SNPs were located within known QTLs or 75 kb near the known SNPs. Five candidate genes (Glyma.05G101800, Glyma.11G140100, Glyma.11G142900, Glyma.19G099700, Glyma.19G100900) in a 90 kb genomic region of each side of four significant SNPs (Gm5_27111367, Gm11_10629613, Gm11_10950924, Gm19_34768458) based on the average LD decay were homologs of Arabidopsis flowering time genes of AT5G48385.1, AT3G46510.1, AT5G59780.3, AT1G28050.1, and AT3G26790.1. These genes encoding FRI (FRIGIDA), PUB13 (plant U-box 13), MYB59, CONSTANS, and FUS3 proteins respectively might play important roles in controlling soybean growth periods. CONCLUSIONS This study identified putative SNP markers associated with soybean growth period traits, which could be used for the marker-assisted selection of soybean growth period traits. Furthermore, the possible candidate genes involved in the control of soybean flowering time were predicted.
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Affiliation(s)
- Minmin Li
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Ying Liu
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Yahan Tao
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Chongjing Xu
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Xin Li
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Xiaoming Zhang
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Xue Yang
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Jingzhe Sun
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Dongmei Li
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
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Atri C, Akhatar J, Gupta M, Gupta N, Goyal A, Rana K, Kaur R, Mittal M, Sharma A, Singh MP, Sandhu PS, Barbetti MJ, Banga SS. Molecular and genetic analysis of defensive responses of Brassica juncea - B. fruticulosa introgression lines to Sclerotinia infection. Sci Rep 2019; 9:17089. [PMID: 31745129 PMCID: PMC6864084 DOI: 10.1038/s41598-019-53444-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 10/31/2019] [Indexed: 12/18/2022] Open
Abstract
Sclerotinia stem rot caused by Sclerotinia sclerotiorum is a major disease of crop brassicas, with inadequate variation for resistance in primary gene pools. We utilized a wild Brassicaceae species with excellent resistance against stem rot to develop a set of B. juncea - B. fruticulosa introgression lines (ILs). These were assessed for resistance using a highly reproducible stem inoculation technique against a virulent pathogen isolate. Over 40% of ILs showed higher levels of resistance. IL-43, IL-175, IL-215, IL-223 and IL-277 were most resistant ILs over three crop seasons. Sequence reads (21x) from the three most diverse ILs were then used to create B. juncea pseudomolecules, by replacing SNPs of reference B. juncea with those of re-sequenced ILs. Genotyping by sequencing (GBS) was also carried out for 88 ILs. Resultant sequence tags were then mapped on to the B. juncea pseudomolecules, and SNP genotypes prepared for each IL. Genome wide association studies helped to map resistance responses to stem rot. A total of 13 significant loci were identified on seven B. juncea chromosomes (A01, A03, A04, A05, A08, A09 and B05). Annotation of the genomic region around identified SNPs allowed identification of 20 candidate genes belonging to major disease resistance protein families, including TIR-NBS-LRR class, Chitinase, Malectin/receptor-like protein kinase, defensin-like (DEFL), desulfoglucosinolate sulfotransferase protein and lipoxygenase. A majority of the significant SNPs could be validated using whole genome sequences (21x) from five advanced generation lines being bred for Sclerotinia resistance as compared to three susceptible B. juncea germplasm lines. Our findings not only provide critical new understanding of the defensive pathway of B. fruticulosa resistance, but will also enable development of marker candidates for assisted transfer of introgressed resistant loci in to agronomically superior cultivars of crop Brassica.
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Affiliation(s)
- Chhaya Atri
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Javed Akhatar
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Mehak Gupta
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Neha Gupta
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Anna Goyal
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Kusum Rana
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Rimaljeet Kaur
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Meenakshi Mittal
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Anju Sharma
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Mohini Prabha Singh
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Prabhjodh S Sandhu
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India
| | - Martin J Barbetti
- School of Agriculture and Environment and the UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Surinder S Banga
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, Punjab, India.
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A SNP Mutation of SiCRC Regulates Seed Number Per Capsule and Capsule Length of cs1 Mutant in Sesame. Int J Mol Sci 2019; 20:ijms20164056. [PMID: 31434218 PMCID: PMC6720709 DOI: 10.3390/ijms20164056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/12/2019] [Accepted: 08/15/2019] [Indexed: 11/16/2022] Open
Abstract
Seed number per capsule (SNC) is a major factor influencing seed yield and is an important trait with complex gene interaction effects. We first performed genetic analysis, gene cloning, and molecular mechanism study for an EMS-induced sesame mutant cs1 with fewer SNC and shorter capsule length (CL). The mutant traits were due to the pleiotropism of a regressive gene (Sics1). Capsule hormone determination showed that five out of 12 hormones, including auxin indole-3-acetic acid (IAA), had significantly different levels between wild type (WT) and mutant type (MT). KEGG pathway analysis showed that plant hormone signal transduction, especially the auxin signal transduction pathway, was the most abundant differentially expressed signaling pathway. After the cross-population association and regional genome screening, we found that three homozygous loci were retained in cs1. Further analysis of these three loci resulted in the identification of SiCRC as the candidate gene for cs1. SiCRC consists of seven exons and six introns encoding 163 amino acids. The SiCRC in cs1 showed a point mutation at intron 5 and exon 6 junction, resulting in the splice site being frame-shifted eight nucleotides further downstream, causing incorrect splicing. Taken together, we assumed the SNP mutation in SiCRC disrupted the function of the transcription factor, which might act downstream of the CRC-auxin signal transduction pathway, resulting in a shorter CL and less SNC mutation of cs1 in sesame. Our results highlight the molecular framework underlying the transcription factor CRC-mediated role of auxin transduction in SNC and CL development.
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Mamo BE, Hayes RJ, Truco MJ, Puri KD, Michelmore RW, Subbarao KV, Simko I. The genetics of resistance to lettuce drop (Sclerotinia spp.) in lettuce in a recombinant inbred line population from Reine des Glaces × Eruption. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2439-2460. [PMID: 31165222 DOI: 10.1007/s00122-019-03365-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/17/2019] [Indexed: 05/08/2023]
Abstract
KEY MESSAGE Two QTLs for resistance to lettuce drop, qLDR1.1 and qLDR5.1, were identified. Associated SNPs will be useful in breeding for lettuce drop and provide the foundation for future molecular analysis. Lettuce drop, caused by Sclerotinia minor and S. sclerotiorum, is an economically important disease of lettuce. The association of resistance to lettuce drop with the commercially undesirable trait of fast bolting has hindered the integration of host resistance in control of this disease. Eruption is a slow-bolting cultivar that exhibits a high level of resistance to lettuce drop. Eruption also is completely resistant to Verticillium wilt caused by race 1 of Verticillium dahliae. A recombinant inbred line population from the cross Reine des Glaces × Eruption was genotyped by sequencing and evaluated for lettuce drop and bolting in separate fields infested with either S. minor or V. dahliae. Two quantitative trait loci (QTLs) for lettuce drop resistance were consistently detected in at least two experiments, and two other QTLs were identified in another experiment; the alleles for resistance at all four QTLs originated from Eruption. A QTL for lettuce drop resistance on linkage group (LG) 5, qLDR5.1, was consistently detected in all experiments and explained 11 to 25% of phenotypic variation. On LG1, qLDR1.1 was detected in two experiments explaining 9 to 12% of the phenotypic variation. Three out of four resistance QTLs are distinct from QTLs for bolting; qLDR5.1 is pleiotropic or closely linked with a QTL for early bolting; however, the rate of bolting shows only a small effect on the variance in resistance observed at this locus. The SNP markers linked with these QTLs will be useful in breeding for resistance through marker-assisted selection.
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Affiliation(s)
- Bullo Erena Mamo
- Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA, 93905, USA
| | - Ryan J Hayes
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, 1636 E. Alisal St, Salinas, CA, 93905, USA
- United States Department of Agriculture, Agricultural Research Service, Forage Seed and Cereal Research Unit, 3450 SW Campus Way, Corvallis, OR, 97321, USA
| | | | - Krishna D Puri
- Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA, 93905, USA
| | - Richard W Michelmore
- UC Davis Genome Center, Davis, CA, 95616, USA
- Departments of Plant Sciences, Molecular and Cellular Biology, Medical Microbiology and Immunology, University of California, Davis, Davis, CA, 95616, USA
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, 1636 E. Alisal St, Salinas, CA, 93905, USA
| | - Ivan Simko
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, 1636 E. Alisal St, Salinas, CA, 93905, USA.
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Wang J, Zhao X, Wang W, Qu Y, Teng W, Qiu L, Zheng H, Han Y, Li W. Genome-wide association study of inflorescence length of cultivated soybean based on the high-throughout single-nucleotide markers. Mol Genet Genomics 2019; 294:607-620. [PMID: 30739204 DOI: 10.1007/s00438-019-01533-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 01/31/2019] [Indexed: 11/25/2022]
Abstract
As an important and complex trait, inflorescence length (IL) of soybean [Glycine max (L.) Merr.] significantly affected seed yields. Therefore, elucidating molecular basis of inflorescence architecture, especially for IL, was important for improving soybean yield potentials. Longer IL meaned to have more pod and seed in soybean. Hence, increasing IL and improving yield are targets for soybean breeding. In this study, a association panel, comprising 283 diverse samples, was used to dissect the genetic basis of IL based on genome-wide association analysis (GWAS) and haplotype analysis. GWAS and haplotype analysis were conducted through high-throughout single-nucleotide polymorphisms (SNP) developed by SLAF-seq methodology. A total of 39, 057 SNPs (minor allele frequency ≥ 0.2 and missing data ≤ 10%) were utilized to evaluate linkage disequilibrium (LD) level in the tested association panel. A total of 30 association signals were identified to be associated with IL via GWAS. Among them, 13 SNPs were novel, and another 17 SNPs were overlapped or located near the linked regions of known quantitative trait nucleotide (QTN) with soybean seed yield or yield component. The functional genes, located in the 200-kb genomic region of each peak SNP, were considered as candidate genes, such as the cell division/ elongation, specific enzymes, and signaling or transport of specific proteins. These genes have been reported to participant in the regulation of IL. Ten typical long-IL lines and ten typical short-IL lines were re-sequencing, and then, six SNPs from five genes were obtained based on candidate gene-based association. In addition, 42 haplotypes were defined based on haplotype analysis. Of them, 11 haplotypes were found to regulate long IL (> 14 mm) in soybean. The identified 30 QTN with beneficial alleles and their candidate genes might be valuable for dissecting the molecular mechanisms of IL and further improving the yield potential of soybean.
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Affiliation(s)
- Jinyang Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Wei Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Yingfan Qu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China
| | - Lijuan Qiu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongkun Zheng
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, 101300, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China.
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China.
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Jiang B, Li M, Cheng Y, Cai Z, Ma Q, Jiang Z, Ma R, Xia Q, Zhang G, Nian H. Genetic mapping of powdery mildew resistance genes in soybean by high-throughput genome-wide sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1833-1845. [PMID: 30826863 DOI: 10.1007/s00122-019-03319-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
KEY MESSAGE The Mendelian locus conferring resistance to powdery mildew in soybean was precisely mapped using a combination of phenotypic screening, genetic analyses, and high-throughput genome-wide sequencing. Powdery mildew (PMD), caused by the fungus Microsphaera diffusa Cooke & Peck, leads to considerable yield losses in soybean [Glycine max (L.) Merr.] under favourable environmental conditions and can be controlled by identifying germplasm resources with resistance genes. In this study, resistance to M. diffusa among resistant varieties B3, Fudou234, and B13 is mapped as a single Mendelian locus using three mapping populations derived from crossing susceptible with resistant cultivars. The position of the PMD resistance locus in B3 is located between simple sequence repeat (SSR) markers GMES6959 and Satt_393 on chromosome 16, at genetic distances of 7.1 cM and 4.6 cM, respectively. To more finely map the PMD resistance gene, a high-density genetic map was constructed using 248 F8 recombinant inbred lines derived from a cross of Guizao1 × B13. The final map includes 3748 bins and is 3031.9 cM in length, with an average distance of 0.81 cM between adjacent markers. This genotypic analysis resulted in the precise delineation of the B13 PMD resistance locus to a 188.06-kb genomic region on chromosome 16 that harbours 28 genes, including 17 disease resistance (R)-like genes in the reference Williams 82 genome. Quantitative real-time PCR assays of possible candidate genes revealed differences in the expression levels of 9 R-like genes between the resistant and susceptible parents. These results provide useful information for marker-assisted breeding and gene cloning for PMD resistance.
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Affiliation(s)
- Bingzhi Jiang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Mu Li
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Yanbo Cheng
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Ze Jiang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Ruirui Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Qiuju Xia
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518086, People's Republic of China
| | - Gengyun Zhang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518086, People's Republic of China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
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Yang X, Yang J, Wang Y, He H, Niu L, Guo D, Xing G, Zhao Q, Zhong X, Sui L, Li Q, Dong Y. Enhanced resistance to sclerotinia stem rot in transgenic soybean that overexpresses a wheat oxalate oxidase. Transgenic Res 2019; 28:103-114. [PMID: 30478526 DOI: 10.1007/s11248-018-0106-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/21/2018] [Indexed: 12/14/2022]
Abstract
Sclerotinia stem rot (SSR), caused by the oxalate-secreting necrotrophic fungal pathogen Sclerotinia sclerotiorum, is one of the devastating diseases that causes significant yield loss in soybean (Glycine max). Until now, effective control of the pathogen is greatly limited by a lack of strong resistance in available commercial soybean cultivars. In this study, transgenic soybean plants overexpressing an oxalic acid (OA)-degrading oxalate oxidase gene OXO from wheat were generated and evaluated for their resistance to S. sclerotiorum. Integration and expression of the transgene were confirmed by Southern and western blot analyses. As compared with non-transformed (NT) control plants, the transgenic lines with increased oxalate oxidase activity displayed significantly reduced lesion sizes, i.e., by 58.71-82.73% reduction of lesion length in a detached stem assay (T3 and T4 generations) and 76.67-82.0% reduction of lesion area in a detached leaf assay (T4 generation). The transgenic plants also showed increased tolerance to the externally applied OA (60 mM) relative to the NT controls. Consecutive resistance evaluation further confirmed an enhanced and stable resistance to S. sclerotiorum in the T3 and T4 transgenic lines. Similarly, decreased OA content and increased hydrogen peroxide (H2O2) levels were also observed in the transgenic leaves after S. sclerotiorum inoculation. Quantitative real-time polymerase chain reaction analysis revealed that the expression level of OXO reached a peak at 1 h and 4 h after inoculation with S. sclerotiorum. In parallel, a significant up-regulation of the hypersensitive response-related genes GmNPR1-1, GmNPR1-2, GmSGT1, and GmRAR occurred, eventually induced by increased release of H2O2 at the infection sites. Interestingly, other defense-related genes such as salicylic acid-dependent genes (GmPR1, GmPR2, GmPR3, GmPR5, GmPR12 and GmPAL), and ethylene/jasmonic acid-dependent genes (GmAOS, GmPPO) also exhibited higher expression levels in the transgenic plants than in the NT controls. Our results demonstrated that overexpression of OXO enhances SSR resistance by degrading OA secreted by S. sclerotiorum and increasing H2O2 levels, and eliciting defense responses mediated by multiple signaling pathways.
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Affiliation(s)
- Xiangdong Yang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Jing Yang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Yisheng Wang
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Hongli He
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Lu Niu
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Dongquan Guo
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Guojie Xing
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Qianqian Zhao
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Xiaofang Zhong
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Li Sui
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Qiyun Li
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| | - Yingshan Dong
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
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Zhao X, Jiang H, Feng L, Qu Y, Teng W, Qiu L, Zheng H, Han Y, Li W. Genome-wide association and transcriptional studies reveal novel genes for unsaturated fatty acid synthesis in a panel of soybean accessions. BMC Genomics 2019; 20:68. [PMID: 30665360 PMCID: PMC6341525 DOI: 10.1186/s12864-019-5449-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 01/11/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The nutritional value of soybean oil is largely influenced by the proportions of unsaturated fatty acids (FAs), including oleic acid (OA, 18:1), linoleic acid (LLA, 18:2), and linolenic acid (LNA, 18:3). Genome-wide association (GWAS) studies along with gene expression studies in soybean [Glycine max (L.) Merr.] were leveraged to dissect the genetics of unsaturated FAs. RESULTS A association panel of 194 diverse soybean accessions were phenotyped in 2013, 2014 and 2015 to identify Single Nucleotide Polymorphisms (SNPs) associated with OA, LLA, and LNA content, and determine putative candidate genes responsible for regulating unsaturated FAs composition. 149 SNPs that represented 73 genomic regions were found to be associated with the unsaturated FA contents in soybean seeds according to the results of GWAS. Twelve novel genes were predicted to be involved in unsaturated FA synthesis in soybean. The relationship between expression pattern of the candidate genes and the accumulation of unsaturated FAs revealed that multiple genes might be involved in unsaturated FAs regulation simultaneously but work in very different ways: Glyma.07G046200 and Glyma.20G245500 promote the OA accumulation in soybean seed in all the tested accessions; Glyma.13G68600 and Glyma.16G200200 promote the OA accumulation only in high OA germplasms; Glyma.07G151300 promotes OA accumulation in higher OA germplasms and suppresses that in lower OA germplasms; Glyma.16G003500 has the effect of increasing LLA accumulation in higher LA germplasms; Glyma.07G254500 suppresses the accumulation of LNA in lower OA germplasms; Glyma.14G194300 might be involved in the accumulation of LNA content in lower LNA germplasms. CONCLUSIONS The beneficial alleles and candidate genes identified might be valuable for improving marker-assisted breeding efficiency and exploring the molecular mechanisms underlying unsaturated fatty acid of soybean.
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Affiliation(s)
- Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, 150030, Harbin, China
| | - Haipeng Jiang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, 150030, Harbin, China
| | - Lei Feng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, 150030, Harbin, China
| | - Yingfan Qu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, 150030, Harbin, China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, 150030, Harbin, China
| | - Lijuan Qiu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hongkun Zheng
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, 101300 China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, 150030, Harbin, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, 150030, Harbin, China
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Zhang C, Li L, Liu Q, Gu L, Huang J, Wei H, Wang H, Yu S. Identification of Loci and Candidate Genes Responsible for Fiber Length in Upland Cotton ( Gossypium hirsutum L.) via Association Mapping and Linkage Analyses. FRONTIERS IN PLANT SCIENCE 2019; 10:53. [PMID: 30804954 PMCID: PMC6370998 DOI: 10.3389/fpls.2019.00053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 01/16/2019] [Indexed: 05/12/2023]
Abstract
Fiber length (FL) is an important fiber quality trait in cotton. Although many fiber quality quantitative trait loci (QTL) responsible for FL have been identified, most cannot be applied to breeding programs, mainly due to unstable environments or large confidence intervals. In this study, we combined a genome-wide association study (GWAS) and linkage mapping to identify and validate high-quality QTLs responsible for FL. For the GWAS, we developed 93,250 high-quality single-nucleotide polymorphism (SNP) markers based on 355 accessions, and the FL was measured in eight different environments. For the linkage mapping, we constructed an F 2 population from two extreme accessions. The high-density linkage maps spanned 3,848.29 cM, with an average marker interval of 1.41 cM. In total, 14 and 13 QTLs were identified in the association and linkage mapping analyses, respectively. Most importantly, a major QTL on chromosome D03 identified in both populations explained more than 10% of the phenotypic variation (PV). Furthermore, we found that a sucrose synthesis-related gene (Gh_D03G1338) was associated with FL in this QTL region. The RNA-seq data showed that Gh_D03G1338 was highly expressed during the fiber development stage, and the qRT-PCR analysis showed significant expression differences between the long fiber and short fiber varieties. These results suggest that Gh_D03G1338 may determine cotton fiber elongation by regulating the synthesis of sucrose. Favorable QTLs and candidate genes should be useful for increasing fiber quality in cotton breeding.
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Affiliation(s)
- Chi Zhang
- College of Agronomy, Northwest A&F University, Yangling, China
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Libei Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qibao Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lijiao Gu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianqin Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shuxun Yu
- College of Agronomy, Northwest A&F University, Yangling, China
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin’an, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- *Correspondence: Shuxun Yu,
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Li D, Zhao X, Han Y, Li W, Xie F. Genome-wide association mapping for seed protein and oil contents using a large panel of soybean accessions. Genomics 2019; 111:90-95. [PMID: 29325965 DOI: 10.1016/j.ygeno.2018.01.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/04/2017] [Accepted: 01/07/2018] [Indexed: 11/17/2022]
Abstract
Soybean is globally cultivated primarily for its protein and oil. The protein and oil contents of the seeds are quantitatively inherited traits determined by the interaction of numerous genes. In order to gain a better understanding of the molecular foundation of soybean protein and oil content for the marker-assisted selection (MAS) of high quality traits, a population of 185 soybean germplasms was evaluated to identify the quantitative trait loci (QTLs) associated with the seed protein and oil contents. Using specific length amplified fragment sequencing (SLAF-seq) technology, a total of 12,072 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) ≥ 0.05 were detected across the 20 chromosomes (Chr), with a marker density of 78.7 kbp. A total of 31 SNPs located on 12 of the 20 soybean chromosomes were correlated with seed protein and oil content. Of the 31 SNPs that were associated with the two target traits, 31 beneficial alleles were identified. Two SNP markers, namely rs15774585 and rs15783346 on Chr 07, were determined to be related to seed oil content both in 2015 and 2016. Three SNP markers, rs53140888 on Chr 01, rs19485676 on Chr 13, and rs24787338 on Chr 20 were correlated with seed protein content both in 2015 and 2016. These beneficial alleles may potentially contribute towards the MAS of favorable soybean protein and oil characteristics.
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Affiliation(s)
- Dongmei Li
- Shenyang Agricultural University, Soybean Research Institute, Shenyang 110866, Liaoning, China
| | - Xue Zhao
- Northeast Agricultural University, Northeastern Key Lab Soybean Biol & Genet & Breed, Chinese Ministry of Agriculture, Key Lab Soybean Biology, Chinese Ministry of Education, Harbin 150030, Heilongjiang, China
| | - Yingpeng Han
- Northeast Agricultural University, Northeastern Key Lab Soybean Biol & Genet & Breed, Chinese Ministry of Agriculture, Key Lab Soybean Biology, Chinese Ministry of Education, Harbin 150030, Heilongjiang, China
| | - Wenbin Li
- Northeast Agricultural University, Northeastern Key Lab Soybean Biol & Genet & Breed, Chinese Ministry of Agriculture, Key Lab Soybean Biology, Chinese Ministry of Education, Harbin 150030, Heilongjiang, China.
| | - Futi Xie
- Shenyang Agricultural University, Soybean Research Institute, Shenyang 110866, Liaoning, China.
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Palumbo F, Qi P, Pinto VB, Devos KM, Barcaccia G. Construction of the First SNP-Based Linkage Map Using Genotyping-by-Sequencing and Mapping of the Male-Sterility Gene in Leaf Chicory. FRONTIERS IN PLANT SCIENCE 2019; 10:276. [PMID: 30915092 PMCID: PMC6421318 DOI: 10.3389/fpls.2019.00276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/20/2019] [Indexed: 05/12/2023]
Abstract
We report the first high-density linkage map construction through genotyping-by-sequencing (GBS) in leaf chicory (Cichorium intybus subsp. intybus var. foliosum, 2n = 2x = 18) and the SNP-based fine mapping of the linkage group region carrying a recessive gene responsible for male-sterility (ms1). An experimental BC1 population, segregating for the male sterility trait, was specifically generated and 198 progeny plants were preliminary screened through a multiplexed SSR genotyping analysis for the identification of microsatellite markers linked to the ms1 locus. Two backbone SSR markers belonging to linkage group 4 of the available Cichorium consensus map were found genetically associated to the ms1 gene at 5.8 and 12.1 cM apart. A GBS strategy was then used to produce a high-density SNP-based linkage map, containing 727 genomic loci organized into 9 linkage groups and spanning a total length of 1,413 cM. 13 SNPs proved to be tightly linked to the ms1 locus based on a subset of 44 progeny plants analyzed. The map position of these markers was further validated by sequence-specific PCR experiments using an additional set of 64 progeny plants, enabling to verify that four of them fully co-segregated with male-sterility. A mesosynteny analysis revealed that 10 genomic DNA sequences encompassing the 13 selected SNPs of chicory mapped in a peripheral region of chromosome 5 of lettuce (Lactuca sativa L.) spanning about 18 Mbp. Since a MYB103-like gene, encoding for a transcription factor involved in callose dissolution of tetrads and exine development of microspores, was found located in the same chromosomal region, this orthologous was chosen as candidate for male-sterility. The amplification and sequencing of its CDS using accessions with contrasting phenotypes/genotypes (i.e., 4 male sterile mutants, ms1ms1, and 4 male fertile inbreds, Ms1Ms1) enabled to detect an INDEL of 4 nucleotides in its second exon, responsible for an anticipated stop codon in the male sterile mutants. This polymorphism was subsequently validated through allele-specific PCR assays and found to fully co-segregate with male-sterility, using 64 progeny plants of the same mapping BC1 population. Overall, our molecular data could be practically exploited for genotyping plant materials and for marker-assisted breeding schemes in leaf chicory.
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Affiliation(s)
- Fabio Palumbo
- Laboratory of Genomics for Plant Breeding, Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
| | - Peng Qi
- Institute of Plant Breeding, Genetics and Genomics, Department of Plant Biology, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | | | - Katrien M. Devos
- Institute of Plant Breeding, Genetics and Genomics, Department of Plant Biology, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Gianni Barcaccia
- Laboratory of Genomics for Plant Breeding, Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Legnaro, Italy
- *Correspondence: Gianni Barcaccia,
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Wang Z, Ma LY, Cao J, Li YL, Ding LN, Zhu KM, Yang YH, Tan XL. Recent Advances in Mechanisms of Plant Defense to Sclerotinia sclerotiorum. FRONTIERS IN PLANT SCIENCE 2019; 10:1314. [PMID: 31681392 PMCID: PMC6813280 DOI: 10.3389/fpls.2019.01314] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/20/2019] [Indexed: 05/20/2023]
Abstract
Sclerotinia sclerotiorum (Lib.) de Bary is an unusual pathogen which has the broad host range, diverse infection modes, and potential double feeding lifestyles of both biotroph and necrotroph. It is capable of infecting over 400 plant species found worldwide and more than 60 names have agriculturally been used to refer to diseases caused by this pathogen. Plant defense to S. sclerotiorum is a complex biological process and exhibits a typical quantitative disease resistance (QDR) response. Recent studies using Arabidopsis thaliana and crop plants have obtained new advances in mechanisms used by plants to cope with S. sclerotiorum infection. In this review, we focused on our current understanding on plant defense mechanisms against this pathogen, and set up a model for the defense process including three stages: recognition of this pathogen, signal transduction and defense response. We also have a particular interest in defense signaling mediated by diverse signaling molecules. We highlight the current challenges and unanswered questions in both the defense process and defense signaling. Essentially, we discussed candidate resistance genes newly mapped by using high-throughput experiments in important crops, and classified these potential gene targets into different stages of the defense process, which will broaden our understanding of the genetic architecture underlying quantitative resistance to S. sclerotiorum. We proposed that more powerful mapping population(s) will be required for accurate and reliable QDR gene identification.
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Zhang H, Miao H, Wei L, Li C, Duan Y, Xu F, Qu W, Zhao R, Ju M, Chang S. Identification of a SiCL1 gene controlling leaf curling and capsule indehiscence in sesame via cross-population association mapping and genomic variants screening. BMC PLANT BIOLOGY 2018; 18:296. [PMID: 30466401 PMCID: PMC6251216 DOI: 10.1186/s12870-018-1503-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 10/26/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Leaf shape can affect plantlet development and seed yield in sesame. The morphological, histological and genetic analyses of a sesame mutant cl1 (cl) with curly leaf and indehiscent capsule traits were performed in this study. In order to clone the cl1 gene for breeding selection, genome re-sequencing of the 130 individuals of cl1 × USA (0)-26 F2 population and a bulked segregation analysis (BSA) pool was carried out. The genome re-sequencing data of the 822 germplasm with normal leaf shape were applied. RESULTS For cl1 mutant, the adaxial/abaxial character of the parenchyma cells in the leaf blades is reduced. Results proved that the leaf curling trait is controlled by a recessive gene (Sicl1). Cross- population association of the F2 population of cl1 × USA (0)-26 indicated that the target cl locus was located on the interval C29 between C29_6522236 and C29_6918901 of SiChr. 1. Further regional genome variants screening determined the 6 candidate variants using genomic variants data of 822 natural germplasm and a BSA pool data. Of which, 5 markers C29_6717525, C29_6721553, C29_6721558, C29_6721563, and C29_6721565 existed in the same gene (C29.460). With the aid of the validation in the test F2 population of cl1 × Yuzhi 11 and natural germplasm, the integrated marker SiCLInDel1 (C29: 6721553-6721572) was determined as the target marker, and C29.460 was the target gene SiCL1 in sesame. SiCL1 is a KAN1 homolog with the full length of 6835 bp. In cl1, the 20 nucleic acids (CAGGTAGCTATGTATATGCA) of SiCLInDel1 marker were mutagenized into 6 nucleic acids (TCTTTG). The deletion led to a frameshift mutation and resulted in the earlier translation termination of the CL gene. The Sicl1 allele was shortened to 1829 bp. SiCL1 gene was expressed mainly in the tissues of stem, leaf, bud, capsule and seed. CONCLUSIONS SiCL1 encodes a transcription repressor KAN1 protein and controls leaf curling and capsule indehiscence in sesame. The findings provided an example of high-efficient gene cloning in sesame. The SiCL1 gene and the cl1 mutant supply the opportunity to explore the development regulation of leaf and capsule, and would improve the new variety breeding with high harvest mechanization adaption in sesame.
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Affiliation(s)
- Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Hongmei Miao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Fangfang Xu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Wenwen Qu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Ruihong Zhao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Ming Ju
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
| | - Shuxian Chang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, 450002 Henan China
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Wen Z, Tan R, Zhang S, Collins PJ, Yuan J, Du W, Gu C, Ou S, Song Q, An YC, Boyse JF, Chilvers MI, Wang D. Integrating GWAS and gene expression data for functional characterization of resistance to white mould in soya bean. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1825-1835. [PMID: 29528555 PMCID: PMC6181214 DOI: 10.1111/pbi.12918] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/31/2018] [Accepted: 02/24/2018] [Indexed: 05/18/2023]
Abstract
White mould of soya bean, caused by Sclerotinia sclerotiorum (Lib.) de Bary, is a necrotrophic fungus capable of infecting a wide range of plants. To dissect the genetic architecture of resistance to white mould, a high-density customized single nucleotide polymorphism (SNP) array (52 041 SNPs) was used to genotype two soya bean diversity panels. Combined with resistance variation data observed in the field and greenhouse environments, genome-wide association studies (GWASs) were conducted to identify quantitative trait loci (QTL) controlling resistance against white mould. Results showed that 16 and 11 loci were found significantly associated with resistance in field and greenhouse, respectively. Of these, eight loci localized to previously mapped QTL intervals and one locus had significant associations with resistance across both environments. The expression level changes in genes located in GWAS-identified loci were assessed between partially resistant and susceptible genotypes through a RNA-seq analysis of the stem tissue collected at various time points after inoculation. A set of genes with diverse biological functionalities were identified as strong candidates underlying white mould resistance. Moreover, we found that genomic prediction models outperformed predictions based on significant SNPs. Prediction accuracies ranged from 0.48 to 0.64 for disease index measured in field experiments. The integrative methods, including GWAS, RNA-seq and genomic selection (GS), applied in this study facilitated the identification of causal variants, enhanced our understanding of mechanisms of white mould resistance and provided valuable information regarding breeding for disease resistance through genomic selection in soya bean.
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Affiliation(s)
- Zixiang Wen
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMIUSA
| | - Ruijuan Tan
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMIUSA
| | - Shichen Zhang
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMIUSA
| | - Paul J. Collins
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMIUSA
| | - Jiazheng Yuan
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMIUSA
- Department of Biological SciencesFayetteville State UniversityFayettevilleNCUSA
| | - Wenyan Du
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMIUSA
| | - Cuihua Gu
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMIUSA
| | - Shujun Ou
- Department of HorticultureMichigan State UniversityEast LansingMIUSA
| | - Qijian Song
- Soya bean Genomics and Improvement LaboratoryUnited States Department of AgricultureAgricultural Research ServiceBeltsvilleMDUSA
| | - Yong‐Qiang Charles An
- USDA‐ARSPlant Genetics Research Unit at Donald Danforth Plant Science CenterSaint LouisMOUSA
| | - John F. Boyse
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMIUSA
| | - Martin I. Chilvers
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMIUSA
| | - Dechun Wang
- Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingMIUSA
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Zatybekov A, Abugalieva S, Didorenko S, Rsaliyev A, Turuspekov Y. GWAS of a soybean breeding collection from South East and South Kazakhstan for resistance to fungal diseases. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Soybean (Glycine max(L.) Merr) is an essential food, feed, and technical culture. In Kazakhstan the area under soybean is increasing every year, helping to solve the problem of protein deficiency in human nutrition and animal feeding. One of the main problems of soybean production is fungal diseases causing yields losses of up to 30 %. Modern genomic studies can be applied to facilitate efficient breeding research for improvement of soybean fungal disease tolerance. Therefore, the objective of this genome-wide association study (GWAS) was analysis of a soybean collection consisting of 182 accessions in relation to fungal diseases in the conditions of South East and South Kazakhstan. Field evaluation of the soybean collection suggested thatFusariumspp. andCercospora sojinaaffected plants in the South region (RIBSP), andSeptoria glycines– in the South East region (KRIAPP). The major objective of the study was identification of QTL associated with resistance to fusarium root rot (FUS), frogeye leaf spot (FLS), and brown spot (BS). GWAS using 4 442 SNP (single nucleotide polymorphism) markers of Illumina iSelect array allowed for identification of fifteen marker trait associations (MTA) resistant to the three diseases at two different stages of growth. Two QTL both for FUS (chromosomes 13 and 17) and BS (chromosomes 14 and 17) were genetically mapped, including one presumably novel QTL for BS (chromosome 17). Also, five presumably novel QTL for FLS were genetically mapped on chromosomes 2, 7, and 15. The results can be used for improvement of the local breeding projects based on marker-assisted selection approach.
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