1
|
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.
Collapse
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.)
| |
Collapse
|
2
|
Silva JNB, Bueno RD, de Sousa TDJF, Xavier YPM, Silva LCC, Piovesan ND, Ribeiro C, Dal-Bianco M. Exploring SoySNP50K and USDA Germplasm Collection Data to Find New QTLs Associated with Protein and Oil Content in Brazilian Genotypes. Biochem Genet 2024:10.1007/s10528-024-10698-5. [PMID: 38358588 DOI: 10.1007/s10528-024-10698-5] [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: 08/30/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
Genetic diversity within a germplasm collection plays a vital role in the success of breeding programs. However, comprehending this diversity and identifying accessions with desirable traits pose significant challenges. This study utilized publicly available data to investigate SNP markers associated with protein and oil content in Brazilian soybeans. Through this research, twenty-two new QTLs (Quantitative Trait Loci) were identified, and we highlighted the substantial influence of Roanoke, Lee and Bragg ancestor on the genetic makeup of Brazilian soybean varieties. Our findings demonstrate that certain markers are being lost in modern cultivars, while others maintain or even increase their frequency. These observations indicate genomic regions that have undergone selection during soybean introduction in Brazil and could be valuable in breeding programs aimed at enhancing protein or oil content.
Collapse
Affiliation(s)
- Jessica Nayara Basílio Silva
- Laboratório de Bioquímica Genética de Plantas, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 21236570-900, Brazil
| | - Rafael Delmond Bueno
- Laboratório de Bioquímica Genética de Plantas, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 21236570-900, Brazil
| | | | - Yan Pablo Moreira Xavier
- Laboratório de Bioquímica Genética de Plantas, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 21236570-900, Brazil
| | - Luiz Claudio Costa Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, BA, 44036-900, Brazil
| | - Newton Deniz Piovesan
- Laboratório de Bioquímica Genética de Plantas, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 21236570-900, Brazil
| | - Cleberson Ribeiro
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Maximiller Dal-Bianco
- Laboratório de Bioquímica Genética de Plantas, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 21236570-900, Brazil.
- Departamento de Bioquímica E Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
| |
Collapse
|
3
|
Wang T, Duan S, Xu C, Wang Y, Zhang X, Xu X, Chen L, Han Z, Wu T. Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits. Nat Commun 2023; 14:7377. [PMID: 37968318 PMCID: PMC10651928 DOI: 10.1038/s41467-023-43270-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023] Open
Abstract
Structural variations (SVs) and copy number variations (CNVs) contribute to trait variations in fleshy-fruited species. Here, we assemble 10 genomes of genetically diverse Malus accessions, including the ever-green cultivar 'Granny Smith' and the widely cultivated cultivar 'Red Fuji'. Combining with three previously reported genomes, we assemble the pan-genome of Malus species and identify 20,220 CNVs and 317,393 SVs. We also observe CNVs that are positively correlated with expression levels of the genes they are associated with. Furthermore, we show that the noncoding RNA generated from a 209 bp insertion in the intron of mitogen-activated protein kinase homology encoding gene, MMK2, regulates the gene expression and affects fruit coloration. Moreover, we identify overlapping SVs associated with fruit quality and biotic resistance. This pan-genome uncovers possible contributions of CNVs to gene expression and highlights the role of SVs in apple domestication and economically important traits.
Collapse
Affiliation(s)
- Ting Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Shiyao Duan
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Chen Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Liyang Chen
- Smartgenomics Technology Institute, Tianjin, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, China.
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China.
| |
Collapse
|
4
|
Potapova NA, Zlobin AS, Perfil’ev RN, Vasiliev GV, Salina EA, Tsepilov YA. Population Structure and Genetic Diversity of the 175 Soybean Breeding Lines and Varieties Cultivated in West Siberia and Other Regions of Russia. PLANTS (BASEL, SWITZERLAND) 2023; 12:3490. [PMID: 37836230 PMCID: PMC10575349 DOI: 10.3390/plants12193490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023]
Abstract
Soybean is a leguminous plant cultivated in many countries and is considered important in the food industry due to the high levels of oil and protein content in the beans. The high demand for soybeans and its products in the industry requires the expansion of cultivation areas. Despite climatic restrictions, West Siberia is gradually expanding its area of soybean cultivation. In this study, we present the first analysis of the population structure and genetic diversity of the 175 soybean Glycine max breeding lines and varieties cultivated in West Siberia (103 accessions) and other regions of Russia (72 accessions), and we compare them with the cultivated soybean varieties from other geographical locations. Principal component analysis revealed several genetic clusters with different levels of genetic heterogeneity. Studied accessions are genetically similar to varieties from China, Japan, and the USA and are genetically distant to varieties from South Korea. Admixture analysis revealed four ancestry groups based on genetic ancestry and geographical origin, which are consistent with the regions of cultivation and origin of accessions and correspond to the principal component analysis result. Population statistics, including nucleotide diversity, Tajima's D, and linkage disequilibrium, are comparatively similar to those observed for studied accessions of a different origin. This study provides essential population and genetic information about the unique collection of breeding lines and varieties cultivated in West Siberia and other Russian regions to foster further evolutionary, genome-wide associations and functional breeding studies.
Collapse
Affiliation(s)
- Nadezhda A. Potapova
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, 127051 Moscow, Russia
| | - Alexander S. Zlobin
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Federal Research Center, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Roman N. Perfil’ev
- Federal Research Center, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Gennady V. Vasiliev
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Federal Research Center, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Elena A. Salina
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Federal Research Center, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Yakov A. Tsepilov
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Federal Research Center, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| |
Collapse
|
5
|
Rani R, Raza G, Tung MH, Rizwan M, Ashfaq H, Shimelis H, Razzaq MK, Arif M. Genetic diversity and population structure analysis in cultivated soybean (Glycine max [L.] Merr.) using SSR and EST-SSR markers. PLoS One 2023; 18:e0286099. [PMID: 37256876 PMCID: PMC10231820 DOI: 10.1371/journal.pone.0286099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/08/2023] [Indexed: 06/02/2023] Open
Abstract
Soybean (Glycine max) is an important legume that is used to fulfill the need of protein and oil of large number of population across the world. There are large numbers of soybean germplasm present in the USDA germplasm resources. Finding and understanding genetically diverse germplasm is a top priority for crop improvement programs. The current study used 20 functional EST-SSR and 80 SSR markers to characterize 96 soybean accessions from diverse geographic backgrounds. Ninety-six of the 100 markers were polymorphic, with 262 alleles (average 2.79 per locus). The molecular markers had an average polymorphic information content (PIC) value of 0.44, with 28 markers ≥ 0.50. The average major allele frequency was 0.57. The observed heterozygosity of the population ranged from 0-0.184 (average 0.02), while the expected heterozygosity ranged from 0.20-0.73 (average 0.51). The lower value for observed heterozygosity than expected heterozygosity suggests the likelihood of a population structure among the germplasm. The phylogenetic analysis and principal coordinate analysis (PCoA) divided the total population into two major groups (G1 and G2), with G1 comprising most of the USA lines and the Australian and Brazilian lines. Furthermore, the phylogenetic analysis and PCoA divided the USA lines into three major clusters without any specific differentiation, supported by the model-based STRUCTURE analysis. Analysis of molecular variance (AMOVA) showed 94% variation among individuals in the total population, with 2% among the populations. For the USA lines, 93% of the variation occurred among individuals, with only 2% among lines from different US states. Pairwise population distance indicated more similarity between the lines from continental America and Australia (189.371) than Asia (199.518). Overall, the 96 soybean lines had a high degree of genetic diversity.
Collapse
Affiliation(s)
- Reena Rani
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Muhammad Haseeb Tung
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Muhammad Rizwan
- Plant Breeding and Genetics Division, Nuclear Institute of Agriculture (NIA), Tandojam, Pakistan
| | - Hamza Ashfaq
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, African Centre for Crop Improvement, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Muhammad Khuram Razzaq
- Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Arif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| |
Collapse
|
6
|
Andrijanić Z, Nazzicari N, Šarčević H, Sudarić A, Annicchiarico P, Pejić I. Genetic Diversity and Population Structure of European Soybean Germplasm Revealed by Single Nucleotide Polymorphism. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091837. [PMID: 37176892 PMCID: PMC10180984 DOI: 10.3390/plants12091837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
Soybean is the most grown high-protein crop in the world. Despite the rapid increase of acreage and production volume, European soybean production accounts for only 34% of its consumption in Europe. This study aims to support the optimal exploitation of genetic resources by European breeding programs by investigating the genetic diversity and the genetic structure of 207 European cultivars or American introductions registered in Europe, which were genotyped by the SoySNP50K array. The expected heterozygosity (He) was 0.34 for the entire collection and ranged among countries from 0.24 for Swiss cultivars to 0.32 for American cultivars (partly reflecting differences in sample size between countries). Cluster analysis grouped all genotypes into two main clusters with eight subgroups that corresponded to the country of origin of cultivars and their maturity group. Pairwise Fst values between countries of origin showed the highest differentiation of Swiss cultivars from the rest of the European gene pool, while the lowest mean differentiation was found between American introductions and all other European countries. On the other hand, Fst values between maturity groups were much lower compared to those observed between countries. In analysis of molecular variance, the total genetic variation was partitioned either by country of origin or by maturity group, explaining 9.1% and 3.5% of the total genetic variance, respectively. On the whole, our results suggest that the European soybean gene pool still has sufficient diversity due to the different historical breeding practices in western and eastern countries and the relatively short period of breeding in Europe.
Collapse
Affiliation(s)
- Zoe Andrijanić
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Svetošimunska Cesta 25, 10000 Zagreb, Croatia
| | - Nelson Nazzicari
- Research Centre for Animal Production and Aquaculture, Council for Agricultural Research and Economics (CREA), Viale Piacenza 29, 26900 Lodi, Italy
| | - Hrvoje Šarčević
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Svetošimunska Cesta 25, 10000 Zagreb, Croatia
- Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000 Zagreb, Croatia
| | - Aleksandra Sudarić
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Svetošimunska Cesta 25, 10000 Zagreb, Croatia
- Agricultural Institute Osijek, Južno Predgrađe 17, 31000 Osijek, Croatia
| | - Paolo Annicchiarico
- Research Centre for Animal Production and Aquaculture, Council for Agricultural Research and Economics (CREA), Viale Piacenza 29, 26900 Lodi, Italy
| | - Ivan Pejić
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Svetošimunska Cesta 25, 10000 Zagreb, Croatia
- Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000 Zagreb, Croatia
| |
Collapse
|
7
|
Shan D, Ali M, Shahid M, Arif A, Waheed MQ, Xia X, Trethowan R, Tester M, Poland J, Ogbonnaya FC, Rasheed A, He Z, Li H. Genetic networks underlying salinity tolerance in wheat uncovered with genome-wide analyses and selective sweeps. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2925-2941. [PMID: 35915266 DOI: 10.1007/s00122-022-04153-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
A genetic framework underpinning salinity tolerance at reproductive stage was revealed by genome-wide SNP markers and major adaptability genes in synthetic-derived wheats, and trait-associated loci were used to predict phenotypes. Using wild relatives of crops to identify genes related to improved productivity and resilience to climate extremes is a prioritized area of crop genetic improvement. High salinity is a widespread crop production constraint, and development of salt-tolerant cultivars is a sustainable solution. We evaluated a panel of 294 wheat accessions comprising synthetic-derived wheat lines (SYN-DERs) and modern bread wheat advanced lines under control and high salinity conditions at two locations. The GWAS analysis revealed a quantitative genetic framework of more than 200 loci with minor effect underlying salinity tolerance at reproductive stage. The significant trait-associated SNPs were used to predict phenotypes using a GBLUP model, and the prediction accuracy (r2) ranged between 0.57 and 0.74. The r2 values for flag leaf weight, days to flowering, biomass, and number of spikes per plant were all above 0.70, validating the phenotypic effects of the loci discovered in this study. Furthermore, the germplasm sets were compared to identify selection sweeps associated with salt tolerance loci in SYN-DERs. Six loci associated with salinity tolerance were found to be differentially selected in the SYN-DERs (12.4 Mb on chromosome (chr)1B, 7.1 Mb on chr2A, 11.2 Mb on chr2D, 200 Mb on chr3D, 600 Mb on chr6B, and 700.9 Mb on chr7B). A total of 228 reported markers and genes, including 17 well-characterized genes, were uncovered using GWAS and EigenGWAS. A linkage disequilibrium (LD) block on chr5A, including the Vrn-A1 gene at 575 Mb and its homeologs on chr5D, were strongly associated with multiple yield-related traits and flowering time under salinity stress conditions. The diversity panel was screened with more than 68 kompetitive allele-specific PCR (KASP) markers of functional genes in wheat, and the pleiotropic effects of superior alleles of Rht-1, TaGASR-A1, and TaCwi-A1 were revealed under salinity stress. To effectively utilize the extensive genetic information obtained from the GWAS analysis, a genetic interaction network was constructed to reveal correlations among the investigated traits. The genetic network data combined with GWAS, selective sweeps, and the functional gene survey provided a quantitative genetic framework for identifying differentially retained loci associated with salinity tolerance in wheat.
Collapse
Affiliation(s)
- Danting Shan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China Office, 12 Zhongguancun South Street, Beijing, 100081, China
- Nanfan Research Institute, CAAS, Sanya, 572024, Hainan, China
| | - Mohsin Ali
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China Office, 12 Zhongguancun South Street, Beijing, 100081, China
- Nanfan Research Institute, CAAS, Sanya, 572024, Hainan, China
| | - Mohammed Shahid
- International Center for Biosaline Agriculture (ICBA), Al Ruwayyah 2, Academic City, Dubai, UAE
| | - Anjuman Arif
- National Institute of Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | | | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China Office, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Richard Trethowan
- Plant Breeding Institute, School of Life and Environmental Sciences, The University of Sydney, Sydney, 2006, Australia
| | - Mark Tester
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KASUT), Thuwal, 23955-6900, Saudi Arabia
| | - Jesse Poland
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KASUT), Thuwal, 23955-6900, Saudi Arabia
- Kansas State University, Manhattan, KS, USA
| | | | - Awais Rasheed
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China Office, 12 Zhongguancun South Street, Beijing, 100081, China.
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China Office, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Huihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China Office, 12 Zhongguancun South Street, Beijing, 100081, China.
- Nanfan Research Institute, CAAS, Sanya, 572024, Hainan, China.
| |
Collapse
|
8
|
Ali M, Danting S, Wang J, Sadiq H, Rasheed A, He Z, Li H. Genetic Diversity and Selection Signatures in Synthetic-Derived Wheats and Modern Spring Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:877496. [PMID: 35903232 PMCID: PMC9315363 DOI: 10.3389/fpls.2022.877496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Synthetic hexaploid wheats and their derived advanced lines were subject to empirical selection in developing genetically superior cultivars. To investigate genetic diversity, patterns of nucleotide diversity, population structure, and selection signatures during wheat breeding, we tested 422 wheat accessions, including 145 synthetic-derived wheats, 128 spring wheat cultivars, and 149 advanced breeding lines from Pakistan. A total of 18,589 high-quality GBS-SNPs were identified that were distributed across the A (40%), B (49%), and D (11%) genomes. Values of population diversity parameters were estimated across chromosomes and genomes. Genome-wide average values of genetic diversity and polymorphic information content were estimated to be 0.30 and 0.25, respectively. Neighbor-joining (NJ) tree, principal component analysis (PCA), and kinship analyses revealed that synthetic-derived wheats and advanced breeding lines were genetically diverse. The 422 accessions were not separated into distinct groups by NJ analysis and confirmed using the PCA. This conclusion was validated with both relative kinship and Rogers' genetic distance analyses. EigenGWAS analysis revealed that 32 unique genome regions had undergone selection. We found that 50% of the selected regions were located in the B-genome, 29% in the D-genome, and 21% in the A-genome. Previously known functional genes or QTL were found within the selection regions associated with phenology-related traits such as vernalization, adaptability, disease resistance, and yield-related traits. The selection signatures identified in the present investigation will be useful for understanding the targets of modern wheat breeding in Pakistan.
Collapse
Affiliation(s)
- Mohsin Ali
- Institute of Crop Sciences and CIMMYT China Office, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Sanya, China
| | - Shan Danting
- Institute of Crop Sciences and CIMMYT China Office, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Sanya, China
| | - Jiankang Wang
- Institute of Crop Sciences and CIMMYT China Office, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Hafsa Sadiq
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Awais Rasheed
- Institute of Crop Sciences and CIMMYT China Office, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zhonghu He
- Institute of Crop Sciences and CIMMYT China Office, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Huihui Li
- Institute of Crop Sciences and CIMMYT China Office, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Sanya, China
| |
Collapse
|
9
|
Genetic and Genomic Resources for Soybean Breeding Research. PLANTS 2022; 11:plants11091181. [PMID: 35567182 PMCID: PMC9101001 DOI: 10.3390/plants11091181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 11/17/2022]
Abstract
Soybean (Glycine max) is a legume species of significant economic and nutritional value. The yield of soybean continues to increase with the breeding of improved varieties, and this is likely to continue with the application of advanced genetic and genomic approaches for breeding. Genome technologies continue to advance rapidly, with an increasing number of high-quality genome assemblies becoming available. With accumulating data from marker arrays and whole-genome resequencing, studying variations between individuals and populations is becoming increasingly accessible. Furthermore, the recent development of soybean pangenomes has highlighted the significant structural variation between individuals, together with knowledge of what has been selected for or lost during domestication and breeding, information that can be applied for the breeding of improved cultivars. Because of this, resources such as genome assemblies, SNP datasets, pangenomes and associated databases are becoming increasingly important for research underlying soybean crop improvement.
Collapse
|
10
|
Mendonça HC, Pereira LFP, Maldonado dos Santos JV, Meda AR, Sant’ Ana GC. Genetic Diversity and Selection Footprints in the Genome of Brazilian Soybean Cultivars. FRONTIERS IN PLANT SCIENCE 2022; 13:842571. [PMID: 35432410 PMCID: PMC9006619 DOI: 10.3389/fpls.2022.842571] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Although Brazil is currently the largest soybean producer in the world, only a small number of studies have analyzed the genetic diversity of Brazilian soybean. These studies have shown the existence of a narrow genetic base. The objectives of this work were to analyze the population structure and genetic diversity, and to identify selection signatures in the genome of soybean germplasms from different companies in Brazil. A panel consisting of 343 soybean lines from Brazil, North America, and Asia was genotyped using genotyping by sequencing (GBS). Population structure was assessed by Bayesian and multivariate approaches. Genetic diversity was analyzed using metrics such as the fixation index, nucleotide diversity, genetic dissimilarity, and linkage disequilibrium. The software BayeScan was used to detect selection signatures between Brazilian and Asian accessions as well as among Brazilian germplasms. Region of origin, company of origin, and relative maturity group (RMG) all had a significant influence on population structure. Varieties belonging to the same company and especially to the same RMG exhibited a high level of genetic similarity. This result was exacerbated among early maturing accessions. Brazilian soybean showed significantly lower genetic diversity when compared to Asian accessions. This was expected, because the crop's region of origin is its main genetic diversity reserve. We identified 7 genomic regions under selection between the Brazilian and Asian accessions, and 27 among Brazilian varieties developed by different companies. Associated with these genomic regions, we found 96 quantitative trait loci (QTLs) for important soybean breeding traits such as flowering, maturity, plant architecture, productivity components, pathogen resistance, and seed composition. Some of the QTLs associated with the markers under selection have genes of great importance to soybean's regional adaptation. The results reported herein allowed to expand the knowledge about the organization of the genetic variability of the Brazilian soybean germplasm. Furthermore, it was possible to identify genomic regions under selection possibly associated with the adaptation of soybean to Brazilian environments.
Collapse
Affiliation(s)
| | - Luiz Filipe Protasio Pereira
- Centro de Ciências Biológicas, State University of Londrina, Londrina, Brazil
- Laboratório de Biotecnologia, Instituto de Desenvolvimento Rural do Paraná, Embrapa Café, Londrina, Brazil
| | | | | | | |
Collapse
|
11
|
Liu N, Niu Y, Zhang G, Feng Z, Bo Y, Lian J, Wang B, Gong Y. Genome sequencing and population resequencing provide insights into the genetic basis of domestication and diversity of vegetable soybean. HORTICULTURE RESEARCH 2022; 9:6498278. [PMID: 35031802 PMCID: PMC8788355 DOI: 10.1093/hr/uhab052] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/26/2021] [Accepted: 08/26/2021] [Indexed: 06/01/2023]
Abstract
Vegetable soybean is one of the most important vegetables in China, and the demand for this vegetable has markedly increased worldwide over the past two decades. Here, we present a high-quality de novo genome assembly of the vegetable soybean cultivar Zhenong 6 (ZN6), which is one of the most popular cultivars in China. The 20 pseudochromosomes cover 94.57% of the total 1.01 Gb assembly size, with contig N50 of 3.84 Mb and scaffold N50 of 48.41 Mb. A total of 55 517 protein-coding genes were annotated. Approximately 54.85% of the assembled genome was annotated as repetitive sequences, with the most abundant long terminal repeat transposable elements. Comparative genomic and phylogenetic analyses with grain soybean Williams 82, six other Fabaceae species and Arabidopsis thaliana genomes highlight the difference of ZN6 with other species. Furthermore, we resequenced 60 vegetable soybean accessions. Alongside 103 previously resequenced wild soybean and 155 previously resequenced grain soybean accessions, we performed analyses of population structure and selective sweep of vegetable, grain, and wild soybean. They were clearly divided into three clades. We found 1112 and 1047 genes under selection in the vegetable soybean and grain soybean populations compared with the wild soybean population, respectively. Among them, we identified 134 selected genes shared between vegetable soybean and grain soybean populations. Additionally, we report four sucrose synthase genes, one sucrose-phosphate synthase gene, and four sugar transport genes as candidate genes related to important traits such as seed sweetness and seed size in vegetable soybean. This study provides essential genomic resources to promote evolutionary and functional genomics studies and genomically informed breeding for vegetable soybean.
Collapse
Affiliation(s)
- Na Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yongchao Niu
- Biozeron Shenzhen, Inc., Shenzhen, 518081, China
| | - Guwen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Zhijuan Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yuanpeng Bo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jinmin Lian
- Biozeron Shenzhen, Inc., Shenzhen, 518081, China
| | - Bin Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yaming Gong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| |
Collapse
|
12
|
Shaibu AS, Ibrahim H, Miko ZL, Mohammed IB, Mohammed SG, Yusuf HL, Kamara AY, Omoigui LO, Karikari B. Assessment of the Genetic Structure and Diversity of Soybean ( Glycine max L.) Germplasm Using Diversity Array Technology and Single Nucleotide Polymorphism Markers. PLANTS (BASEL, SWITZERLAND) 2021; 11:68. [PMID: 35009071 PMCID: PMC8747349 DOI: 10.3390/plants11010068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 11/20/2022]
Abstract
Knowledge of the genetic structure and diversity of germplasm collections is crucial for sustainable genetic improvement through hybridization programs and rapid adaptation to changing breeding objectives. The objective of this study was to determine the genetic diversity and population structure of 281 International Institute of Tropical Agriculture (IITA) soybean accessions using diversity array technology (DArT) and single nucleotide polymorphism (SNP) markers for the efficient utilization of these accessions. From the results, the SNP and DArT markers were well distributed across the 20 soybean chromosomes. The cluster and principal component analyses revealed the genetic diversity among the 281 accessions by grouping them into two stratifications, a grouping that was also evident from the population structure analysis, which divided the 281 accessions into two distinct groups. The analysis of molecular variance revealed that 97% and 98% of the genetic variances using SNP and DArT markers, respectively, were within the population. Genetic diversity indices such as Shannon's diversity index, diversity and unbiased diversity revealed the diversity among the different populations of the soybean accessions. The SNP and DArT markers used provided similar information on the structure, diversity and polymorphism of the accessions, which indicates the applicability of the DArT marker in genetic diversity studies. Our study provides information about the genetic structure and diversity of the IITA soybean accessions that will allow for the efficient utilization of these accessions in soybean improvement programs, especially in Africa.
Collapse
Affiliation(s)
- Abdulwahab S. Shaibu
- Department of Agronomy, Bayero University Kano, Kano 700001, Nigeria; (H.I.); (Z.L.M.); (I.B.M.)
| | - Hassan Ibrahim
- Department of Agronomy, Bayero University Kano, Kano 700001, Nigeria; (H.I.); (Z.L.M.); (I.B.M.)
| | - Zainab L. Miko
- Department of Agronomy, Bayero University Kano, Kano 700001, Nigeria; (H.I.); (Z.L.M.); (I.B.M.)
| | - Ibrahim B. Mohammed
- Department of Agronomy, Bayero University Kano, Kano 700001, Nigeria; (H.I.); (Z.L.M.); (I.B.M.)
| | - Sanusi G. Mohammed
- Centre for Dryland Agriculture, Bayero University Kano, Kano 700001, Nigeria;
| | - Hauwa L. Yusuf
- Department of Food Science and Technology, Bayero University Kano, Kano 700001, Nigeria;
| | - Alpha Y. Kamara
- International Institute of Tropical Agriculture, Ibadan 200211, Nigeria; (A.Y.K.); (L.O.O.)
| | - Lucky O. Omoigui
- International Institute of Tropical Agriculture, Ibadan 200211, Nigeria; (A.Y.K.); (L.O.O.)
| | - Benjamin Karikari
- Department of Crop Science, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, P.O. Box TL 1882, Tamale 00233, Ghana;
| |
Collapse
|
13
|
Czembor E, Czembor JH, Suchecki R, Watson-Haigh NS. DArT-based evaluation of soybean germplasm from Polish Gene Bank. BMC Res Notes 2021; 14:343. [PMID: 34461984 PMCID: PMC8404325 DOI: 10.1186/s13104-021-05750-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 08/18/2021] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE Soybean is an important plant used for food, feed and many industrial purposes. Interest in soybean breeding is growing in Central Europe, including Poland. A very large number of soybean accessions are stored in gene banks, but less than 1% of them have been used for breeding. Here, we present genotypic data as well as phenotypic data on plant and seed performance, including seed chlorophyll fluorescence traits, and on yield components within a collection of soybean accessions that are conserved in the Polish Gene Bank at the Plant Breeding and Acclimatization Institute-National Research Institute. RESULTS The materials used consisted of sub-collections: 79 Polish genotypes, including old traditional cultivars, 24 Canadian, 21 American, 21 Swedish and 31 from Central and Eastern European Countries, 9 from France and 6 from Japan. In total, 9602 high quality SNPs were derived from DArTseq, a method utilising GBS technology. GWAS, performed with the BLINK model, revealed that a total of 41 significant SNPs were mapped for days to flowering, flower colour, plant height, days to pod formation, 100 seed weight, pod colour, seeds and hilum colour and steady-state chlorophyll fluorescence under light (Ft_Lss). This is the first report about the diversity of traditional old Polish soybean cultivars.
Collapse
Affiliation(s)
- Elzbieta Czembor
- Plant Breeding and Acclimatization Institute-NRI, Radzikow, Blonie, Poland
| | - Jerzy H Czembor
- Plant Breeding and Acclimatization Institute-NRI, Radzikow, Blonie, Poland
| | | | - Nathan S Watson-Haigh
- South Australian Genomics Centre, SAHMRI, North Terrace, Adelaide, SA, 5000, Australia.
- Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, Melbourne, VIC, 3000, Australia.
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.
- Genome Informatics & Bioinformatics Training, Flagstaff Hill, SA, 5159, Australia.
| |
Collapse
|
14
|
Qi GA, Zheng YT, Lin F, Huang X, Duan LW, You Y, Liu H, Wang Y, Xu HM, Chen GB. EigenGWAS: An online visualizing and interactive application for detecting genomic signatures of natural selection. Mol Ecol Resour 2021; 21:1732-1744. [PMID: 33665976 DOI: 10.1111/1755-0998.13370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/17/2021] [Accepted: 02/25/2021] [Indexed: 11/30/2022]
Abstract
Detecting genetic regions under selection in structured populations is of great importance in ecology, evolutionary biology and breeding programmes. We recently proposed EigenGWAS, an unsupervised genomic scanning approach that is similar to F ST but does not require grouping information of the population, for detection of genomic regions under selection. The original EigenGWAS is designed for the random mating population, and here we extend its use to inbred populations. We also show in theory and simulation that eigenvalues, the previous corrector for genetic drift in EigenGWAS, are overcorrected for genetic drift, and the genomic inflation factor is a better option for this adjustment. Applying the updated algorithm, we introduce the new EigenGWAS online platform with highly efficient core implementation. Our online computational tool accepts plink data in a standard binary format that can be easily converted from the original sequencing data, provides the users with graphical results via the R-Shiny user-friendly interface. We applied the proposed method and tool to various data sets, and biologically interpretable results as well as caveats that may lead to an unsatisfactory outcome are given. The EigenGWAS online platform is available at www.eigengwas.com, and can be localized and scaled up via R (recommended) or docker.
Collapse
Affiliation(s)
- Guo-An Qi
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuan-Ting Zheng
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Feng Lin
- Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Xin Huang
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Li-Wen Duan
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yue You
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hailan Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ying Wang
- Phase I Clinical Research Center, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Hai-Ming Xu
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guo-Bo Chen
- Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China.,Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, People's Hospital of Hangzhou Medical College, Hangzhou, China
| |
Collapse
|
15
|
Saleem A, Muylle H, Aper J, Ruttink T, Wang J, Yu D, Roldán-Ruiz I. A Genome-Wide Genetic Diversity Scan Reveals Multiple Signatures of Selection in a European Soybean Collection Compared to Chinese Collections of Wild and Cultivated Soybean Accessions. FRONTIERS IN PLANT SCIENCE 2021; 12:631767. [PMID: 33732276 PMCID: PMC7959735 DOI: 10.3389/fpls.2021.631767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/01/2021] [Indexed: 05/03/2023]
Abstract
Targeted and untargeted selections including domestication and breeding efforts can reduce genetic diversity in breeding germplasm and create selective sweeps in crop genomes. The genomic regions at which selective sweeps are detected can reveal important information about signatures of selection. We have analyzed the genetic diversity within a soybean germplasm collection relevant for breeding in Europe (the EUCLEG collection), and have identified selective sweeps through a genome-wide scan comparing that collection to Chinese soybean collections. This work involved genotyping of 480 EUCLEG soybean accessions, including 210 improved varieties, 216 breeding lines and 54 landraces using the 355K SoySNP microarray. SNP calling of 477 EUCLEG accessions together with 328 Chinese soybean accessions identified 224,993 high-quality SNP markers. Population structure analysis revealed a clear differentiation between the EUCLEG collection and the Chinese materials. Further, the EUCLEG collection was sub-structured into five subgroups that were differentiated by geographical origin. No clear association between subgroups and maturity group was detected. The genetic diversity was lower in the EUCLEG collection compared to the Chinese collections. Selective sweep analysis revealed 23 selective sweep regions distributed over 12 chromosomes. Co-localization of these selective sweep regions with previously reported QTLs and genes revealed that various signatures of selection in the EUCLEG collection may be related to domestication and improvement traits including seed protein and oil content, phenology, nitrogen fixation, yield components, diseases resistance and quality. No signatures of selection related to stem determinacy were detected. In addition, absence of signatures of selection for a substantial number of QTLs related to yield, protein content, oil content and phenological traits suggests the presence of substantial genetic diversity in the EUCLEG collection. Taken together, the results obtained demonstrate that the available genetic diversity in the EUCLEG collection can be further exploited for research and breeding purposes. However, incorporation of exotic material can be considered to broaden its genetic base.
Collapse
Affiliation(s)
- Aamir Saleem
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Hilde Muylle
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Jonas Aper
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Jiao Wang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Deyue Yu
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Isabel Roldán-Ruiz
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- *Correspondence: Isabel Roldán-Ruiz,
| |
Collapse
|
16
|
Song Q, Yan L, Quigley C, Fickus E, Wei H, Chen L, Dong F, Araya S, Liu J, Hyten D, Pantalone V, Nelson RL. Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:800-811. [PMID: 32772442 PMCID: PMC7702105 DOI: 10.1111/tpj.14960] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/30/2020] [Indexed: 05/10/2023]
Abstract
The limited number of recombinant events in recombinant inbred lines suggests that for a biparental population with a limited number of recombinant inbred lines, it is unnecessary to genotype the lines with many markers. For genomic prediction and selection, previous studies have demonstrated that only 1000-2000 genome-wide common markers across all lines/accessions are needed to reach maximum efficiency of genomic prediction in populations. Evaluation of too many markers will not only increase the cost but also generate redundant information. We developed a soybean (Glycine max) assay, BARCSoySNP6K, containing 6000 markers, which were carefully chosen from the SoySNP50K assay based on their position in the soybean genome and haplotype block, polymorphism among accessions and genotyping quality. The assay includes 5000 single nucleotide polymorphisms (SNPs) from euchromatic and 1000 from heterochromatic regions. The percentage of SNPs with minor allele frequency >0.10 was 95% and 91% in the euchromatic and heterochromatic regions, respectively. Analysis of progeny from two large families genotyped with SoySNP50K versus BARCSoySNP6K showed that the position of the common markers and number of unique bins along linkage maps were consistent based on the SNPs genotyped with the two assays; however, the rate of redundant markers was dramatically reduced with the BARCSoySNP6K. The BARCSoySNP6K assay is proven as an excellent tool for detecting quantitative trait loci, genomic selection and assessing genetic relationships. The assay is commercialized by Illumina Inc. and being used by soybean breeders and geneticists and the list of SNPs in the assay is an ideal resource for SNP genotyping by targeted amplicon sequencing.
Collapse
Affiliation(s)
- Qijian Song
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - Long Yan
- Shijiazhuang Branch Center of National Center for Soybean Improvement/the Key Laboratory of Crop Genetics and BreedingInstitute of Cereal and Oil CropsHebei Academy of Agricultural and Forestry SciencesShijiazhuangChina
| | - Charles Quigley
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - Edward Fickus
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - He Wei
- Institute of Industrial CropsHenan Academy of Agricultural SciencesZhengzhouHenan ProvinceChina
| | - Linfeng Chen
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - Faming Dong
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - Susan Araya
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - Jinlong Liu
- Soybean Genomics and Improvement Lab.USDA‐ARSBeltsvilleMDUSA
| | - David Hyten
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | | | - Randall L. Nelson
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit and Department of Crop SciencesUSDA‐ARSUniversity of IllinoisUrbanaILUSA
| |
Collapse
|
17
|
Abstract
AbstractAmong the weedy plant species, Johnsongrass (Sorghum halepense) is one of the most destructive. Johnsongrass has invaded new habitats beyond its native Eurasian origin by outcompeting native flora and cultivated crops. The Johnsongrass habitat is expanding continuously due to clonal and self-pollinating reproduction strategy, accelerated growth and the progressing climate change. As a result, Johnsongrass has reduced native plant diversity in grasslands and inflicted economic damage to agriculture on every continent. Johnsongrass is a growing threat to crop production, as it serves as a refuge for a variety of agricultural pests and plant viral diseases. Over the past decades, herbicides extensively applied to control Johnsongrass have boosted selection pressure, resulting in the independent evolution of herbicide-resistant ecotypes across multiple locations. The apparent threat to native flora and agriculture caused by the invasive Johnsongrass is a subject to a long and ongoing research. This review provides a historical and research overview on Johnsongrass expansion, its current as well future impact particularly on North American and European grasslands and agriculture.
Collapse
|
18
|
Liu Y, Du H, Li P, Shen Y, Peng H, Liu S, Zhou GA, Zhang H, Liu Z, Shi M, Huang X, Li Y, Zhang M, Wang Z, Zhu B, Han B, Liang C, Tian Z. Pan-Genome of Wild and Cultivated Soybeans. Cell 2020; 182:162-176.e13. [PMID: 32553274 DOI: 10.1016/j.cell.2020.05.023] [Citation(s) in RCA: 392] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 04/07/2020] [Accepted: 05/12/2020] [Indexed: 12/21/2022]
Abstract
Soybean is one of the most important vegetable oil and protein feed crops. To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced accessions. Using these assembled genomes together with three previously reported genomes, we constructed a graph-based genome and performed pan-genome analysis, which identified numerous genetic variations that cannot be detected by direct mapping of short sequence reads onto a single reference genome. The structural variations from the 2,898 accessions that were genotyped based on the graph-based genome and the RNA sequencing (RNA-seq) data from the representative 26 accessions helped to link genetic variations to candidate genes that are responsible for important traits. This pan-genome resource will promote evolutionary and functional genomics studies in soybean.
Collapse
Affiliation(s)
- Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengcheng Li
- Berry Genomics Corporation, Beijing 100015, China
| | - Yanting Shen
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Hua Peng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Guo-An Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | | | - Zhi Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Miao Shi
- Berry Genomics Corporation, Beijing 100015, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yan Li
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Baoge Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
19
|
Pavan S, Delvento C, Ricciardi L, Lotti C, Ciani E, D'Agostino N. Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies. Front Genet 2020; 11:447. [PMID: 32587600 PMCID: PMC7299185 DOI: 10.3389/fgene.2020.00447] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 04/14/2020] [Indexed: 12/19/2022] Open
Abstract
High-throughput genotyping boosts genome-wide association studies (GWAS) in crop species, leading to the identification of single-nucleotide polymorphisms (SNPs) associated with economically important traits. Choosing a cost-effective genotyping method for crop GWAS requires careful examination of several aspects, namely, the purpose and the scale of the study, crop-specific genomic features, and technical and economic matters associated with each genotyping option. Once genotypic data have been obtained, quality control (QC) procedures must be applied to avoid bias and false signals in genotype–phenotype association tests. QC for human GWAS has been extensively reviewed; however, QC for crop GWAS may require different actions, depending on the GWAS population type. Here, we review most popular genotyping methods based on next-generation sequencing (NGS) and array hybridization, and report observations that should guide the investigator in the choice of the genotyping method for crop GWAS. We provide recommendations to perform QC in crop species, and deliver an overview of bioinformatics tools that can be used to accomplish all needed tasks. Overall, this work aims to provide guidelines to harmonize those procedures leading to SNP datasets ready for crop GWAS.
Collapse
Affiliation(s)
- Stefano Pavan
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy.,Institute of Biomedical Technologies, National Research Council (CNR), Bari, Italy
| | - Chiara Delvento
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Concetta Lotti
- Department of Agricultural, Food and Environmental Sciences, University of Foggia, Foggia, Italy
| | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Bari, Italy
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
| |
Collapse
|
20
|
Tang Z, Fu Y, Xu J, Zhu M, Li X, Yu M, Zhao S, Liu X. Discovery of selection-driven genetic differences of Duroc, Landrace, and Yorkshire pig breeds by EigenGWAS and F st analyses. Anim Genet 2020; 51:531-540. [PMID: 32400898 DOI: 10.1111/age.12946] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2020] [Indexed: 01/08/2023]
Abstract
Pigs are one of the earliest domesticated animals and multiple breeds have been developed to meet the various demands of consumers. EigenGWAS is a novel strategy to identify candidate genes that underlying population genetic differences and to infer candidate regions under selection as well. In this study, EigenGWAS and Fst analyses were performed using the public re-sequencing data of three typical commercial pig breeds, Duroc, Landrace and Yorkshire. The intersection of genome-wide significant SNPs detected by EigenGWAS and top-ranked 1% SNPs of Fst results were treated as signals under selection. Using the data of all three breeds, 3062 signals under selection were detected and the nearby genomic regions within 300 kb upstream and downstream covered 6.54% of whole genome. Pairs of breeds were analysed along with the pathway analysis. The gene function enrichment results indicated that many candidate genes located in the genomic regions of the signals under selection were associated with biological processes related to growth, metabolism, reproduction, sensory perception, etc. Among the candidate genes, the FSHB, AHR, PTHLH, KDR and FST genes were reported to be associated with reproductive performance; the KIT, KITLG, MITF, MC1R and EDNRB genes were previously identified to affect coat colour; the RETREG1, TXNIP, BMP5, PPARD and RBP4 genes were reported to be associated with lipid metabolism and growth traits. The identified genetic differences across the three commercial breeds will advance understanding of the artificial selection history of pigs and the signals under selection will suggest potential uses in pig genomic breeding programmes.
Collapse
Affiliation(s)
- Z Tang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Y Fu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, 430070, China
| | - J Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - M Zhu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - X Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - M Yu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - S Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - X Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, Hubei, 430070, China.,Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| |
Collapse
|
21
|
Liu Z, Li H, Gou Z, Zhang Y, Wang X, Ren H, Wen Z, Kang BK, Li Y, Yu L, Gao H, Wang D, Qi X, Qiu L. Genome-wide association study of soybean seed germination under drought stress. Mol Genet Genomics 2020; 295:661-673. [PMID: 32008123 DOI: 10.1007/s00438-020-01646-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 01/09/2020] [Indexed: 10/25/2022]
Abstract
Drought stress, which is increasing with climate change, is a serious threat to agricultural sustainability worldwide. Seed germination is an essential growth phase that ensures the successful establishment and productivity of soybean, which can lose substantial productivity in soils with water deficits. However, only limited genetic information is available about how germinating soybean seeds may exert drought tolerance. In this study, we examined the germinating seed drought-tolerance phenotypes and genotypes of a panel of 259 released Chinese soybean cultivars panel. Based on 4616 Single-Nucleotide Polymorphisms (SNPs), we conducted a mixed-linear model GWAS that identified a total of 15 SNPs associated with at least one drought-tolerance index. Notably, three of these SNPs were commonly associated with two drought-tolerance indices. Two of these SNPs are positioned upstream of genes, and 11 of them are located in or near regions where QTLs have been previously mapped by linkage analysis, five of which are drought-related. The SNPs detected in this study can both drive hypothesis-driven research to deepen our understanding of genetic basis of soybean drought tolerance at the germination stage and provide useful genetic resources that can facilitate the selection of drought stress traits via genomic-assisted selection.
Collapse
Affiliation(s)
- Zhangxiong Liu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huihui Li
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zuowang Gou
- Institute of Crop Sciences, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Yanjun Zhang
- Institute of Crop Sciences, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Xingrong Wang
- Institute of Crop Sciences, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Honglei Ren
- Maize Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Zixiang Wen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, 48824, USA
| | - Beom-Kyu Kang
- Upland Crop Breeding Research Division, Department of Southern Area Crop Science, National Institute of Crop Science, Miryang, 52402, Korea
| | - Yinghui Li
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lili Yu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huawei Gao
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, 48824, USA
| | - Xusheng Qi
- Institute of Crop Sciences, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Lijuan Qiu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
22
|
Karikari B, Bhat JA, Denwar NN, Zhao T. Exploring the genetic base of the soybean germplasm from Africa, America and Asia as well as mining of beneficial allele for flowering and seed weight. 3 Biotech 2020; 10:195. [PMID: 32296618 DOI: 10.1007/s13205-020-02186-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/30/2020] [Indexed: 11/26/2022] Open
Abstract
Genetic diversity is the foundation for any breeding program. The present study analyzed the genetic base of 163 soybean genotypes from three continents viz. Africa, America and Asia using 68 trait-linked simple sequence repeats (SSR) markers. The average number of alleles among the germplasm from the three continents followed the trend as Asia (9) > America (8) > Africa (7). Similar trends were observed for gene diversity (0.76 > 0.74 > 0.71) and polymorphism information content (PIC) (0.73 > 0.71 > 0.68). These findings revealed that soybean germplasm from Asia has wider genetic base followed by America, and least in Africa. The 163 genotypes were grouped into 4 clusters by phylogenetic analysis, whereas model-based population structure analysis also divided them into 4 subpopulations comprising 80.61% pure lines and 19.39% admixtures. The genotypes from Africa were easily distinguished from those of other two continents using phylogenetic analysis, indicating important role of geographyical differentiation for this genetic variability. Our results indicated that soybean germplasm has moved from Asia to America, and from America to Africa. Analysis of molecular variance (AMOVA) showed 8.41% variation among the four subpopulations, whereas 63.12% and 28.47% variation existed among and within individuals in the four subpopulations, respectively. Based on the association mapping, a total of 21 SSR markers showed significant association with days to flowering (DoF) and 100-seed weight (HSW). Two markers Satt365 and Satt581 on chromosome 6 and 10, respectively, showed pleiotropic effect or linkage on both traits. Genotype A50 (Gakuran Daizu/PI 506679) from Japan has 8 out of the 13 beneficial alleles for increased HSW. The diverse genotypes, polymorphic SSR markers and desirable alleles identified for DoF and HSW will be used in future breeding programs to improve reproductive, yield and quality traits.
Collapse
Affiliation(s)
- Benjamin Karikari
- 1MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Javaid A Bhat
- 1MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Nicholas N Denwar
- Council of Scientific and Industrial Research-Savanna Agricultural Research Institute, Tamale, Ghana
| | - Tuanjie Zhao
- 1MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), National Centre for Soybean Improvement, State Key Laboratory for Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| |
Collapse
|
23
|
Serendipitous In Situ Conservation of Faba Bean Landraces in Tunisia: A Case Study. Genes (Basel) 2020; 11:genes11020236. [PMID: 32102450 PMCID: PMC7074078 DOI: 10.3390/genes11020236] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 12/19/2022] Open
Abstract
Cultivation of faba bean (Vicia faba L.) in Tunisia is largely based on improved varieties of the crop. However, a few farmers continue to produce local cultivars or landraces. The National Gene Bank of Tunisia (NGBT) recently launched a collection project for faba bean landraces, with special focus on the regions of the North West, traditionally devoted to cultivating grain legumes, and where around 80% of the total national faba bean cultivation area is located. The seed phenotypic features of the collected samples were studied, and the genetic diversity and population structure analyzed using simple sequence repeat markers. The genetic constitution of the present samples was compared to that of faba bean samples collected by teams of the International Center for Agricultural Research in the Dry Areas (ICARDA) in the 1970s in the same region, and stored at the ICARDA gene bank. The results of the diversity analysis demonstrate that the recently collected samples and those stored at ICARDA largely overlap, thus demonstrating that over the past 50 years, little genetic change has occurred to the local faba bean populations examined. These findings suggest that farmers serendipitously applied international best practices for in situ conservation of agricultural crops.
Collapse
|
24
|
Boakyewaa Adu G, Badu-Apraku B, Akromah R, Garcia-Oliveira AL, Awuku FJ, Gedil M. Genetic diversity and population structure of early-maturing tropical maize inbred lines using SNP markers. PLoS One 2019; 14:e0214810. [PMID: 30964890 PMCID: PMC6456193 DOI: 10.1371/journal.pone.0214810] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/20/2019] [Indexed: 11/23/2022] Open
Abstract
Information on genetic diversity and population structure are very important in any breeding programme for the improvement of traits of interest and the development of outstanding products for commercialization. In the present study, we assessed the genetic diversity of 94 early-maturing white and yellow tropical maize inbred lines using single nucleotide polymorphism (SNP) markers. The larger number of SNP markers used in this study allowed a clearer inference of the population structure of the 94 inbred lines. Cluster analysis resolved the inbred lines into different clusters based on their pedigree, selection history and endosperm colour. However, three heterotic groups were revealed by population structure analysis, but additional field evaluation could be more informative to confirm the heterotic groups identified. Nevertheless, wide genetic variability existed among the inbred lines making them unique with the potential to contribute new beneficial alleles to maize breeding programmes in the tropics, especially in the West and Central Africa (WCA) sub-region.
Collapse
Affiliation(s)
| | - Baffour Badu-Apraku
- International Institute of Tropical Agriculture (UK) Limited, Carolyn House, Croydon, United Kignodm
- * E-mail:
| | - Richard Akromah
- Department of Crop and Soil Sciences, Faculty of Agriculture, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | | | - Melaku Gedil
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| |
Collapse
|
25
|
Shen Y, Liu J, Geng H, Zhang J, Liu Y, Zhang H, Xing S, Du J, Ma S, Tian Z. De novo assembly of a Chinese soybean genome. SCIENCE CHINA. LIFE SCIENCES 2018; 61:871-884. [PMID: 30062469 DOI: 10.1007/s11427-018-9360-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 07/05/2018] [Indexed: 10/28/2022]
Abstract
Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high-quality soybean reference genome from this area is critical for soybean research and breeding. Here, we report the de novo assembly and sequence analysis of a Chinese soybean genome for "Zhonghuang 13" by a combination of SMRT, Hi-C and optical mapping data. The assembled genome size is 1.025 Gb with a contig N50 of 3.46 Mb and a scaffold N50 of 51.87 Mb. Comparisons between this genome and the previously reported reference genome (cv. Williams 82) uncovered more than 250,000 structure variations. A total of 52,051 protein coding genes and 36,429 transposable elements were annotated for this genome, and a gene co-expression network including 39,967 genes was also established. This high quality Chinese soybean genome and its sequence analysis will provide valuable information for soybean improvement in the future.
Collapse
Affiliation(s)
- Yanting Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jing Liu
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Haiying Geng
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Jixiang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | | | - Shilai Xing
- Berry Genomics Corporation, Beijing, 100015, China
| | - Jianchang Du
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Shisong Ma
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100039, China.
| |
Collapse
|