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Jiang Y, Dong L, Li H, Liu Y, Wang X, Liu G. Genetic linkage map construction and QTL analysis for plant height in proso millet (Panicum miliaceum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:78. [PMID: 38466414 DOI: 10.1007/s00122-024-04576-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/06/2024] [Indexed: 03/13/2024]
Abstract
KEY MESSAGE A genetic linkage map representing proso millet genome was constructed with SSR markers, and a major QTL corresponding to plant height was mapped on chromosome 14 of this map. Proso millet (Panicum miliaceum L.) has the lowest water requirements of all cultivated cereal crops. However, the lack of a genetic map and the paucity of genomic resources for this species have limited the utility of proso millet for detailed genetic studies and hampered genetic improvement programs. In this study, 97,317 simple sequence repeat (SSR) markers were developed based on the genome sequence of the proso millet landrace Longmi 4. Using some of these markers in conjunction with previously identified SSRs, an SSR-based linkage map for proso millet was successfully constructed using a large mapping population (316 F2 offspring). In total, 186 SSR markers were assigned to 18 linkage groups corresponding to the haploid chromosomes. The constructed map had a total length of 3033.42 centimorgan (cM) covering 78.17% of the assembled reference genome. The length of the 18 linkage groups ranged from 88.89 cM (Chr. 15) to 274.82 cM (Chr. 16), with an average size of 168.17 cM. To our knowledge, this is the first genetic linkage map for proso millet based on SSR markers. Plant height is one of the most important traits in crop improvement. A major QTL was repeatedly detected in different environments, explaining 8.70-24.50% of the plant height variations. A candidate gene affecting auxin biosynthesis and transport, and ROS homeostasis regulation was predicted. Thus, the linkage map and QTL analysis provided herein will promote the development of gene mining and molecular breeding in proso millet.
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Affiliation(s)
- Yanmiao Jiang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Li Dong
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Haiquan Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Yanan Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China
| | - Xindong Wang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, Hebei, China.
- Key Laboratory of Minor Crops in Hebei, Shijiazhuang, 050035, Hebei, China.
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Menamo T, Borrell AK, Mace E, Jordan DR, Tao Y, Hunt C, Kassahun B. Genetic dissection of root architecture in Ethiopian sorghum landraces. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:209. [PMID: 37715848 DOI: 10.1007/s00122-023-04457-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 08/28/2023] [Indexed: 09/18/2023]
Abstract
KEY MESSAGE This study quantified genetic variation in root system architecture (root number, angle, length and dry mass) within a diversity panel of 1771 Ethiopian sorghum landraces and identified 22 genomic regions associated with the root variations. The root system architecture (RSA) of crop plants influences adaptation to water-limited conditions and determines the capacity of a plant to access soil water and nutrients. Four key root traits (number, angle, length and dry mass) were evaluated in a diversity panel of 1771 Ethiopian sorghum landraces using purpose-built root chambers. Significant genetic variation was observed in all studied root traits, with nodal root angle ranging from 16.4° to 26.6°, with a high repeatability of 78.9%. Genome wide association studies identified a total of 22 genomic regions associated with root traits which were distributed on all chromosomes except chromosome SBI-10. Among the 22 root genomic regions, 15 co-located with RSA trait QTL previously identified in sorghum, with the remaining seven representing novel RSA QTL. The majority (85.7%) of identified root angle QTL also co-localized with QTL previously identified for stay-green in sorghum. This suggests that the stay-green phenotype might be associated with root architecture that enhances water extraction during water stress conditions. The results open avenues for manipulating root phenotypes to improve productivity in abiotic stress environments via marker-assisted selection.
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Affiliation(s)
- Temesgen Menamo
- College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
| | - Andrew K Borrell
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Emma Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, Hermitage Research Facility, Warwick, QLD, 4370, Australia
- Agri-Science Queensland, Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - David R Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Colleen Hunt
- Agri-Science Queensland, Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Bantte Kassahun
- College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia.
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Kamal NM, Gorafi YSA, Tomemori H, Kim JS, Elhadi GMI, Tsujimoto H. Genetic variation for grain nutritional profile and yield potential in sorghum and the possibility of selection for drought tolerance under irrigated conditions. BMC Genomics 2023; 24:515. [PMID: 37660014 PMCID: PMC10474746 DOI: 10.1186/s12864-023-09613-w] [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] [Received: 03/28/2023] [Accepted: 08/22/2023] [Indexed: 09/04/2023] Open
Abstract
BACKGROUND Increasing grain nutritional value in sorghum (Sorghum bicolor) is a paramount breeding objective, as is increasing drought resistance (DR), because sorghum is grown mainly in drought-prone areas. The genetic basis of grain nutritional traits remains largely unknown. Marker-assisted selection using significant loci identified through genome-wide association study (GWAS) shows potential for selecting desirable traits in crops. This study assessed natural variation available in sorghum accessions from around the globe to identify novel genes or genomic regions with potential for improving grain nutritional value, and to study associations between DR traits and grain weight and nutritional composition. RESULTS We dissected the genetic architecture of grain nutritional composition, protein content, thousand-kernel weight (TKW), and plant height (PH) in sorghum through GWAS of 163 unique African and Asian accessions under irrigated and post-flowering drought conditions. Several QTLs were detected. Some were significantly associated with DR, TKW, PH, protein, and Zn, Mn, and Ca contents. Genomic regions on chromosomes 1, 2, 4, 8, 9, and 10 were associated with TKW, nutritional, and DR traits; colocalization patterns of these markers indicate potential for simultaneous improvement of these traits. In African accessions, markers associated with TKW were mapped to six regions also associated with protein, Zn, Ca, Mn, Na, and DR, suggesting the potential for simultaneous selection for higher grain nutrition and TKW. Our results indicate that it may be possible to select for increased DR on the basis of grain nutrition and weight potential. CONCLUSIONS This study provides a valuable resource for selecting landraces for use in plant breeding programs and for identifying loci that may contribute to grain nutrition and weight with the hope of producing cultivars that combine improved yield traits, nutrition, and DR.
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Affiliation(s)
- Nasrein Mohamed Kamal
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
- Agricultural Research Corporation, PO Box 126, Wad Medani, Sudan.
| | - Yasir Serag Alnor Gorafi
- Agricultural Research Corporation, PO Box 126, Wad Medani, Sudan
- International Platform for Dryland Research and Education, Tottori University, Tottori, Japan
| | - Hisashi Tomemori
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan
| | - June-Sik Kim
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | | | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
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Dweikat IM, Gelli M, Bernards M, Martin A, Jhala A. Mutations in the acetolactate synthase (ALS) enzyme affect shattercane (Sorghum bicolor) response to ALS-inhibiting herbicides. Hereditas 2023; 160:28. [PMID: 37344897 DOI: 10.1186/s41065-023-00291-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 06/09/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND Shattercane [Sorghum bicolor (L.) Moench ssp. Arundinaceum (Desv.)] is a competitive weed in North America's corn, soybean, sorghum, and other agronomic crops. Control of shattercane with POST herbicides in corn became possible with the introduction of acetolactate synthase (ALS)-inhibiting herbicides in the 1980s, and their extensive use resulted in the evolution of ALS-inhibitors resistant shattercane. RESULTS Shattercane seeds were collected from 16 south-eastern and south-central Nebraska fields that were treated with primisulfuron for three consecutive years. Three resistant plants were found in greenhouse evaluations of more than 30,000 plants. Results from a greenhouse bioassay conducted to assess the response of each shattercane biotype to ALS-inhibiting herbicides showed a differential response to ALS inhibitors within and between chemical classes. Biotype P8-30 was resistant or partially resistant to all ALS-inhibiting herbicides applied and displayed a unique amino acid sequence substitution (Trp574 to Leu) relative to the other two resistant biotypes, P2-205 and P9-102. Whole plant dose-response studies confirmed a 4- to the 12-fold level of primisulfuron resistance in three shattercane biotypes compared with the known primisulfuron-susceptible shattercane biotype. The ALS gene was sequenced using primers designed from the corn ALS sequence to identify mutations in the ALS gene that confer resistance. A total of seven nucleotide substitutions were detected in the three herbicide-resistant biotypes P2-205, P8-30, and P9-102. These biotypes are being crossed to adapted sorghum lines (grain, sweet, and forage) to broaden germplasm with resistance to ALS-inhibiting herbicides. CONCLUSION The discovery of these mutants should accelerate the development of sorghum genotypes that tolerate ALS-based herbicides, which provide additional choices for sorghum farmers to control weeds, especially grasses, in their fields.
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Affiliation(s)
- Ismail M Dweikat
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
| | - Malleswari Gelli
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Mark Bernards
- Department of Agronomy, Crop Science and Weed Control, Western Illinois University, Macomb, IL, 61455, USA
| | - Alex Martin
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Amit Jhala
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
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Wang L, Shang L, Wu X, Hao H, Jing HC. Genomic architecture of leaf senescence in sorghum (Sorghum bicolor). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:45. [PMID: 36905488 DOI: 10.1007/s00122-023-04315-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
Leaf senescence in sorghum is primarily controlled by the progression, but not by the onset of senescence. The senescence-delaying haplotypes of 45 key genes accentuated from landraces to improved lines. Leaf senescence is a genetically programmed developmental process and plays a central role for plant survival and crop production by remobilising nutrients accumulated in senescent leaves. In theory, the ultimate outcome of leaf senescence is determined by the onset and progression of senescence, but how these two processes contribute to senescence is not fully illustrated in crops and the genetic basis for them is not well understood. Sorghum (Sorghum bicolor), which is known for the remarkable stay-green trait, is ideal for dissecting the genomic architecture underlying the regulation of senescence. In this study, a diverse panel of 333 sorghum lines was explored for the onset and progression of leaf senescence. Trait correlation analysis showed that the progression of leaf senescence, rather than the onset of leaf senescence, significantly correlated with variations of the final leaf greenness. This notion was further supported by GWAS, which identified 31 senescence-associated genomic regions containing 148 genes, of which 124 were related to the progression of leaf senescence. The senescence-delaying haplotypes of 45 key candidate genes were enriched in lines with extremely prolonged senescence duration, while senescence-promoting haplotypes in those with extremely accelerated senescence. Haplotype combinations of these genes could well explain the segregation of the senescence trait in a recombinant inbred population. We also demonstrated that senescence-delaying haplotypes of candidate genes were under strong selection during sorghum domestication and genetic improvement. Together, this research advanced our understanding of crop leaf senescence and provided a suite of candidate genes for functional genomics and molecular breeding.
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Affiliation(s)
- Lidong Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Shang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaoyuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Huaiqing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Engineering Laboratory for Grass-Based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits. Biochem Soc Trans 2022; 50:583-596. [PMID: 35212360 PMCID: PMC9022969 DOI: 10.1042/bst20210908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/01/2022] [Accepted: 02/14/2022] [Indexed: 12/18/2022]
Abstract
DNA methylation is a chromatin modification that plays an essential role in regulating gene expression and genome stability and it is typically associated with gene silencing and heterochromatin. Owing to its heritability, alterations in the patterns of DNA methylation have the potential to provide for epigenetic inheritance of traits. Contemporary epigenomic technologies provide information beyond sequence variation and could supply alternative sources of trait variation for improvement in crops such as sorghum. Yet, compared with other species such as maize and rice, the sorghum DNA methylome is far less well understood. The distribution of CG, CHG, and CHH methylation in the genome is different compared with other species. CG and CHG methylation levels peak around centromeric segments in the sorghum genome and are far more depleted in the gene dense chromosome arms. The genes regulating DNA methylation in sorghum are also yet to be functionally characterised; better understanding of their identity and functional analysis of DNA methylation machinery mutants in diverse genotypes will be important to better characterise the sorghum methylome. Here, we catalogue homologous genes encoding methylation regulatory enzymes in sorghum based on genes in Arabidopsis, maize, and rice. Discovering variation in the methylome may uncover epialleles that provide extra information to explain trait variation and has the potential to be applied in epigenome-wide association studies or genomic prediction. DNA methylation can also improve genome annotations and discover regulatory elements underlying traits. Thus, improving our knowledge of the sorghum methylome can enhance our understanding of the molecular basis of traits and may be useful to improve sorghum performance.
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Zhi X, Tao Y, Jordan D, Borrell A, Hunt C, Cruickshank A, Potgieter A, Wu A, Hammer G, George-Jaeggli B, Mace E. Genetic control of leaf angle in sorghum and its effect on light interception. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:801-816. [PMID: 34698817 DOI: 10.1093/jxb/erab467] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
Developing sorghum genotypes adapted to different light environments requires understanding of a plant's ability to capture light, determined through leaf angle specifically. This study dissected the genetic basis of leaf angle in 3 year field trials at two sites, using a sorghum diversity panel (729 accessions). A wide range of variation in leaf angle with medium heritability was observed. Leaf angle explained 36% variation in canopy light extinction coefficient, highlighting the extent to which variation in leaf angle influences light interception at the whole-canopy level. This study also found that the sorghum races of Guinea and Durra consistently having the largest and smallest leaf angle, respectively, highlighting the potential role of leaf angle in adaptation to distinct environments. The genome-wide association study detected 33 quantitative trait loci (QTLs) associated with leaf angle. Strong synteny was observed with previously detected leaf angle QTLs in maize (70%) and rice (40%) within 10 cM, among which the overlap was significantly enriched according to χ2 tests, suggesting a highly consistent genetic control in grasses. A priori leaf angle candidate genes identified in maize and rice were found to be enriched within a 1-cM window around the sorghum leaf angle QTLs. Additionally, protein domain analysis identified the WD40 protein domain as being enriched within a 1-cM window around the QTLs. These outcomes show that there is sufficient heritability and natural variation in the angle of upper leaves in sorghum which may be exploited to change light interception and optimize crop canopies for different contexts.
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Affiliation(s)
- Xiaoyu Zhi
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
| | - Andrew Borrell
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
| | - Colleen Hunt
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Warwick, QLD, Australia
| | - Alan Cruickshank
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Warwick, QLD, Australia
| | - Andries Potgieter
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, QLD, Australia
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Gatton, QLD, Australia
| | - Alex Wu
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, QLD, Australia
| | - Graeme Hammer
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, St Lucia, QLD, Australia
| | - Barbara George-Jaeggli
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Warwick, QLD, Australia
| | - Emma Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, Warwick, QLD, Australia
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Warwick, QLD, Australia
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Monkhan T, Chen X, Somta P. BADH1 is associated with fragrance in sorghum (Sorghum bicolor (L.) Moench) cultivar ‘Ambemohor’. J Genet 2021. [DOI: 10.1007/s12041-020-01256-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Wang X, Mace E, Tao Y, Cruickshank A, Hunt C, Hammer G, Jordan D. Large-scale genome-wide association study reveals that drought-induced lodging in grain sorghum is associated with plant height and traits linked to carbon remobilisation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3201-3215. [PMID: 32833037 DOI: 10.1007/s00122-020-03665-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
KEY MESSAGE We detected 213 lodging QTLs and demonstrated that drought-induced stem lodging in grain sorghum is substantially associated with stay-green and plant height suggesting a critical role of carbon remobilisation. Sorghum is generally grown in water limited conditions and often lodges under post-anthesis drought, which reduces yield and quality. Due to its complexity, our understanding on the genetic control of lodging is very limited. We dissected the genetic architecture of lodging in grain sorghum through genome-wide association study (GWAS) on 2308 unique hybrids grown in 17 Australian sorghum trials over 3 years. The GWAS detected 213 QTLs, the majority of which showed a significant association with leaf senescence and plant height (72% and 71%, respectively). Only 16 lodging QTLs were not associated with either leaf senescence or plant height. The high incidence of multi-trait association for the lodging QTLs indicates that lodging in grain sorghum is mainly associated with plant height and traits linked to carbohydrate remobilisation. This result supported the selection for stay-green (delayed leaf senescence) to reduce lodging susceptibility, rather than selection for short stature and lodging resistance per se, which likely reduces yield. Additionally, our data suggested a protective effect of stay-green on weakening the association between lodging susceptibility and plant height. Our study also showed that lodging resistance might be improved by selection for stem composition but was unlikely to be improved by selection for classical resistance to stalk rots.
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Affiliation(s)
- Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, 4370, Australia
| | - Emma Mace
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, 4370, Australia
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Warwick, QLD, 4370, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, 4370, Australia
| | - Alan Cruickshank
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Warwick, QLD, 4370, Australia
| | - Colleen Hunt
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, 4370, Australia
- Agri-Science Queensland, Department of Agriculture and Fisheries (DAF), Warwick, QLD, 4370, Australia
| | - Graeme Hammer
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, 4370, Australia.
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Genomic Dissection of Anthracnose ( Colletotrichum sublineolum) Resistance Response in Sorghum Differential Line SC112-14. G3-GENES GENOMES GENETICS 2020; 10:1403-1412. [PMID: 32102832 PMCID: PMC7144069 DOI: 10.1534/g3.120.401121] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sorghum production is expanding to warmer and more humid regions where its production is being limited by multiple fungal pathogens. Anthracnose, caused by Colletotrichum sublineolum, is one of the major diseases in these regions, where it can cause yield losses of both grain and biomass. In this study, 114 recombinant inbred lines (RILs) derived from resistant sorghum line SC112-14 were evaluated at four distinct geographic locations in the United States for response to anthracnose. A genome scan using a high-density linkage map of 3,838 single nucleotide polymorphisms (SNPs) detected two loci at 5.25 and 1.18 Mb on chromosomes 5 and 6, respectively, that explain up to 59% and 44% of the observed phenotypic variation. A bin-mapping approach using a subset of 31 highly informative RILs was employed to determine the disease response to inoculation with ten anthracnose pathotypes in the greenhouse. A genome scan showed that the 5.25 Mb region on chromosome 5 is associated with a resistance response to nine pathotypes. Five SNP markers were developed and used to fine map the locus on chromosome 5 by evaluating 1,500 segregating F2:3 progenies. Based on the genotypic and phenotypic analyses of 11 recombinants, the locus was narrowed down to a 470-kb genomic region. Following a genome-wide association study based on 574 accessions previously phenotyped and genotyped, the resistance locus was delimited to a 34-kb genomic interval with five candidate genes. All five candidate genes encode proteins associated with plant immune systems, suggesting they may act in synergy in the resistance response.
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Tao Y, Zhao X, Wang X, Hathorn A, Hunt C, Cruickshank AW, van Oosterom EJ, Godwin ID, Mace ES, Jordan DR. Large-scale GWAS in sorghum reveals common genetic control of grain size among cereals. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1093-1105. [PMID: 31659829 PMCID: PMC7061873 DOI: 10.1111/pbi.13284] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/30/2019] [Accepted: 10/24/2019] [Indexed: 05/20/2023]
Abstract
Grain size is a key yield component of cereal crops and a major quality attribute. It is determined by a genotype's genetic potential and its capacity to fill the grains. This study aims to dissect the genetic architecture of grain size in sorghum. An integrated genome-wide association study (GWAS) was conducted using a diversity panel (n = 837) and a BC-NAM population (n = 1421). To isolate genetic effects associated with genetic potential of grain size, rather than the genotype's capacity to fill the grains, a treatment of removing half of the panicle was imposed during flowering. Extensive and highly heritable variation in grain size was observed in both populations in 5 field trials, and 81 grain size QTL were identified in subsequent GWAS. These QTL were enriched for orthologues of known grain size genes in rice and maize, and had significant overlap with SNPs associated with grain size in rice and maize, supporting common genetic control of this trait among cereals. Grain size genes with opposite effect on grain number were less likely to overlap with the grain size QTL from this study, indicating the treatment facilitated identification of genetic regions related to the genetic potential of grain size. These results enhance understanding of the genetic architecture of grain size in cereal, and pave the way for exploration of underlying molecular mechanisms and manipulation of this trait in breeding practices.
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Affiliation(s)
- Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Xianrong Zhao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Adrian Hathorn
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
| | - Colleen Hunt
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
- Agri‐Science QueenslandDepartment of Agriculture and Fisheries (DAF)Hermitage Research FacilityWarwickQldAustralia
| | - Alan W. Cruickshank
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
- Agri‐Science QueenslandDepartment of Agriculture and Fisheries (DAF)Hermitage Research FacilityWarwickQldAustralia
| | - Erik J. van Oosterom
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandBrisbaneQldAustralia
| | - Ian D. Godwin
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandBrisbaneQldAustralia
| | - Emma S. Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
- Agri‐Science QueenslandDepartment of Agriculture and Fisheries (DAF)Hermitage Research FacilityWarwickQldAustralia
| | - David R. Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI)The University of QueenslandHermitage Research FacilityWarwickQldAustralia
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Ananda GKS, Myrans H, Norton SL, Gleadow R, Furtado A, Henry RJ. Wild Sorghum as a Promising Resource for Crop Improvement. FRONTIERS IN PLANT SCIENCE 2020; 11:1108. [PMID: 32765575 PMCID: PMC7380247 DOI: 10.3389/fpls.2020.01108] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/06/2020] [Indexed: 05/21/2023]
Abstract
Sorghum bicolor (L.) Moench is a multipurpose food crop which is ranked among the top five cereal crops in the world, and is used as a source of food, fodder, feed, and fuel. The genus Sorghum consists of 24 diverse species. Cultivated sorghum was derived from the wild progenitor S. bicolor subsp. verticilliflorum, which is commonly distributed in Africa. Archeological evidence has identified regions in Sudan, Ethiopia, and West Africa as centers of origin of sorghum, with evidence for more than one domestication event. The taxonomy of the genus is not fully resolved, with alternative classifications that should be resolved by further molecular analysis. Sorghum can withstand severe droughts which makes it suitable to grow in regions where other major crops cannot be grown. Wild relatives of many crops have played significant roles as genetic resources for crop improvement. Although there have been many studies of domesticated sorghum, few studies have reported on its wild relatives. In Sorghum, some species are widely distributed while others are very restricted. Of the 17 native sorghum species found in Australia, none have been cultivated. Isolation of these wild species from domesticated crops makes them a highly valuable system for studying the evolution of adaptive traits such as biotic and abiotic stress tolerance. The diversity of the genus Sorghum has probably arisen as a result of the extensive variability of the habitats over which they are distributed. The wild gene pool of sorghum may, therefore, harbor many useful genes for abiotic and biotic stress tolerance. While there are many examples of successful examples of introgression of novel alleles from the wild relatives of other species from Poaceae, such as rice, wheat, maize, and sugarcane, studies of introgression from wild sorghum are limited. An improved understanding of wild sorghums will better allow us to exploit this previously underutilized gene pool for the production of more resilient crops.
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Affiliation(s)
- Galaihalage K. S. Ananda
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Harry Myrans
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Sally L. Norton
- Australian Grains Genebank, Agriculture Victoria, Horsham, VIC, Australia
| | - Roslyn Gleadow
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- *Correspondence: Robert J. Henry,
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Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population. G3-GENES GENOMES GENETICS 2019; 9:4045-4057. [PMID: 31611346 PMCID: PMC6893202 DOI: 10.1534/g3.119.400353] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Dissecting the genetic architecture of stress tolerance in crops is critical to understand and improve adaptation. In temperate climates, early planting of chilling-tolerant varieties could provide longer growing seasons and drought escape, but chilling tolerance (<15°) is generally lacking in tropical-origin crops. Here we developed a nested association mapping (NAM) population to dissect the genetic architecture of early-season chilling tolerance in the tropical-origin cereal sorghum (Sorghum bicolor [L.] Moench). The NAM resource, developed from reference line BTx623 and three chilling-tolerant Chinese lines, is comprised of 771 recombinant inbred lines genotyped by sequencing at 43,320 single nucleotide polymorphisms. We phenotyped the NAM population for emergence, seedling vigor, and agronomic traits (>75,000 data points from ∼16,000 plots) in multi-environment field trials in Kansas under natural chilling stress (sown 30-45 days early) and normal growing conditions. Joint linkage mapping with early-planted field phenotypes revealed an oligogenic architecture, with 5-10 chilling tolerance loci explaining 20-41% of variation. Surprisingly, several of the major chilling tolerance loci co-localize precisely with the classical grain tannin (Tan1 and Tan2) and dwarfing genes (Dw1 and Dw3) that were under strong directional selection in the US during the 20th century. These findings suggest that chilling sensitivity was inadvertently selected due to coinheritance with desired nontannin and dwarfing alleles. The characterization of genetic architecture with NAM reveals why past chilling tolerance breeding was stymied and provides a path for genomics-enabled breeding of chilling tolerance.
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Kotla A, Phuke R, Hariprasanna K, Mehtre SP, Rathore A, Gorthy S, Srivastava RK, Das R, Bhanu Prakash A, Radhika K, Hash CT, Reddy BV, Patil J, Jabeen F, Shashikanth D, Jaganathan J, Gaddameedi A, Subhasini V, Deshpande SP, Kumar AA. Identification of QTLs and candidate genes for high grain Fe and Zn concentration in sorghum [Sorghum bicolor (L.)Moench]. J Cereal Sci 2019. [DOI: 10.1016/j.jcs.2019.102850] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Liu H, Liu H, Zhou L, Lin Z. Genetic Architecture of domestication- and improvement-related traits using a population derived from Sorghum virgatum and Sorghum bicolor. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:135-146. [PMID: 31128683 DOI: 10.1016/j.plantsci.2019.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/16/2019] [Accepted: 02/22/2019] [Indexed: 06/09/2023]
Abstract
The genetic basis of domestication and improvement remains largely unknown in sorghum as a typical multiple-origins species. In this study, the F2 and F3 populations derived from a cross between Sorghum virgatum and domesticated sorghum were used to study the genetic architecture of domestication- and improvement-related traits. We found that human selection had greatly reshaped sorghum through the Quantitative Trait Loci (QTLs) with large genetic effects in the traits of harvest, plant architecture and grain taste including the reduction of shattering, few branches, short plant stature and the removal of polyphenols from seed. The expansion of seed width was selected to improve the yield through accumulating small-effect QTLs. Two major QTLs of plant height (QTI-ph1 and dw1) were narrowed down into 24.5-kilobase (kb) and 13.9-kb, respectively. DNA diversity analysis and association mapping of dw1 gene suggested the functional variant (A1361 T) might originate from the same event not long time ago. Our results supported that parallel phenotypic changes across different species during domestication and improvement might share the same genetic basis, QTL × QTL interactions might not play an important role in the reshaping of traits during sorghum domestication and improvement, and offered new views on transgressive segregation and segregation distortion. Our study greatly deepens our understandings of the genetic basis of sorghum domestication and improvement.
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Affiliation(s)
- Huanhuan Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, Department of Plant Genomics and Bioinformatics, China Agricultural University, Beijing 100193, China
| | - Hangqin Liu
- National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, Department of Plant Genomics and Bioinformatics, China Agricultural University, Beijing 100193, China
| | - Leina Zhou
- National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, Department of Plant Genomics and Bioinformatics, China Agricultural University, Beijing 100193, China
| | - Zhongwei Lin
- National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, Department of Plant Genomics and Bioinformatics, China Agricultural University, Beijing 100193, China.
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Cormier F, Lawac F, Maledon E, Gravillon MC, Nudol E, Mournet P, Vignes H, Chaïr H, Arnau G. A reference high-density genetic map of greater yam (Dioscorea alata L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1733-1744. [PMID: 30783744 PMCID: PMC6531416 DOI: 10.1007/s00122-019-03311-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/11/2019] [Indexed: 05/19/2023]
Abstract
This study generated the first high-density genetic map for D. alata based on genotyping-by-sequencing and provides new insight on sex determination in yam. Greater yam (Dioscorea alata L.) is a major staple food in tropical and subtropical areas. This study aimed to produce the first reference genetic map of this dioecious species using genotyping-by-sequencing. In this high-density map combining information of two F1 outcrossed populations, 20 linkage groups were resolved as expected and 1579 polymorphic markers were ordered. The consensus map length was 2613.5 cM with an average SNP interval of 1.68 cM. An XX/XY sex determination system was identified on LG6 via the study of sex ratio, homology of parental linkage groups and the identification of a major QTL for sex determination. Homology with the sequenced D. rotundata is described, and the median physical distance between SNPs was estimated at 139.1 kb. The effects of segregation distortion and the presence of heteromorphic sex chromosomes are discussed. This D. alata linkage map associated with the available genomic resources will facilitate quantitative trait mapping, marker-assisted selection and evolutionary studies in the important yet scarcely studied yam species.
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Affiliation(s)
- Fabien Cormier
- CIRAD, UMR AGAP, 97170, Petit-Bourg, Guadeloupe, France.
- Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
| | - Floriane Lawac
- CIRAD, UMR AGAP, 97170, Petit-Bourg, Guadeloupe, France
- Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- VARTC, P.O. Box 231, Luganville, Santo, Vanuatu
| | - Erick Maledon
- CIRAD, UMR AGAP, 97170, Petit-Bourg, Guadeloupe, France
- Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Marie-Claire Gravillon
- CIRAD, UMR AGAP, 97170, Petit-Bourg, Guadeloupe, France
- Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Elie Nudol
- CIRAD, UMR AGAP, 97170, Petit-Bourg, Guadeloupe, France
- Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Pierre Mournet
- CIRAD, UMR AGAP, 97170, Petit-Bourg, Guadeloupe, France
- CIRAD, UMR AGAP, 34398, Montpellier, France
| | - Hélène Vignes
- CIRAD, UMR AGAP, 97170, Petit-Bourg, Guadeloupe, France
- CIRAD, UMR AGAP, 34398, Montpellier, France
| | - Hâna Chaïr
- CIRAD, UMR AGAP, 97170, Petit-Bourg, Guadeloupe, France
- CIRAD, UMR AGAP, 34398, Montpellier, France
| | - Gemma Arnau
- CIRAD, UMR AGAP, 97170, Petit-Bourg, Guadeloupe, France
- Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
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Prom LK, Ahn E, Isakeit T, Magill C. GWAS analysis of sorghum association panel lines identifies SNPs associated with disease response to Texas isolates of Colletotrichum sublineola. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1389-1396. [PMID: 30688991 DOI: 10.1007/s00122-019-03285-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 01/16/2019] [Indexed: 05/27/2023]
Abstract
SNPs identify prospective genes related to response to Colletotrichum sublineola (anthracnose) in the sorghum association panel lines. Sorghum association panel (SAP) lines were scored over several years for response to Colletotrichum sublineola, the causal agent of the disease anthracnose. Known resistant and susceptible lines were included each year to verify successful inoculation. Over 79,000 single-nucleotide polymorphic (SNP) loci from a publicly available genotype by sequencing dataset available for the SAP lines were used with TASSEL association mapping software to identify chromosomal locations associated with differences in disease response. When the top-scoring SNPs were mapped to the published sorghum genome, in each case, the nearest annotated gene has precedence for a role in host defense.
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Affiliation(s)
- Louis K Prom
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, 77845, USA.
| | - Ezekiel Ahn
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Thomas Isakeit
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
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Unraveling the genetic complexity underlying sorghum response to water availability. PLoS One 2019; 14:e0215515. [PMID: 30998785 PMCID: PMC6472798 DOI: 10.1371/journal.pone.0215515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/28/2019] [Indexed: 11/19/2022] Open
Abstract
Understanding the adaptation mechanisms of sorghum to drought and the underlying genetic architecture may help to improve its production in a wide range of environments. By crossing a high yielding parent (HYP) and a drought tolerant parent (DTP), we obtained 140 recombinant inbred lines (RILs), which were genotyped with 120 DArT and SSR markers covering 14 linkage groups (LGs). A subset of 100 RILs was evaluated three times in control and drought treatments to genetically dissect their response to water availability. Plants with early heading date (HD) in the drought treatment maintained yield (YLD) level by reducing seed number SN and increasing hundred seed weight (HSW). In contrast, early HD in the control treatment increased SN, HSW and YLD. In total, 133 significant QTL associated with the measured traits were detected in ten hotspot regions. Antagonistic, pleiotropic effects of a QTL cluster mapped on LG-6 may explain the observed trade-offs between SN and HSW: Alleles from DTP reduced SN and the alleles from HYP increased HSW under drought stress, but not in the control treatment. Our results illustrate the importance of considering genetic and environmental factors in QTL mapping to better understand plant responses to drought and to improve breeding programs.
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Mace E, Innes D, Hunt C, Wang X, Tao Y, Baxter J, Hassall M, Hathorn A, Jordan D. The Sorghum QTL Atlas: a powerful tool for trait dissection, comparative genomics and crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:751-766. [PMID: 30343386 DOI: 10.1007/s00122-018-3212-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/11/2018] [Indexed: 05/20/2023]
Abstract
We describe the development and application of the Sorghum QTL Atlas, a high-resolution, open-access research platform to facilitate candidate gene identification across three cereal species, sorghum, maize and rice. The mechanisms governing the genetic control of many quantitative traits are only poorly understood and have yet to be fully exploited. Over the last two decades, over a thousand QTL and GWAS studies have been published in the major cereal crops including sorghum, maize and rice. A large body of information has been generated on the genetic basis of quantitative traits, their genomic location, allelic effects and epistatic interactions. However, such QTL information has not been widely applied by cereal improvement programs and genetic researchers worldwide. In part this is due to the heterogeneous nature of QTL studies which leads QTL reliability variation from study to study. Using approaches to adjust the QTL confidence interval, this platform provides access to the most updated sorghum QTL information than any database available, spanning 23 years of research since 1995. The QTL database provides information on the predicted gene models underlying the QTL CI, across all sorghum genome assembly gene sets and maize and rice genome assemblies and also provides information on the diversity of the underlying genes and information on signatures of selection in sorghum. The resulting high-resolution, open-access research platform facilitates candidate gene identification across 3 cereal species, sorghum, maize and rice. Using a number of trait examples, we demonstrate the power and resolution of the resource to facilitate comparative genomics approaches to provide a bridge between genomics and applied breeding.
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Affiliation(s)
- Emma Mace
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia.
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia.
| | - David Innes
- Department of Agriculture and Fisheries, Ecosciences Precinct, Brisbane, QLD, 4102, Australia
| | - Colleen Hunt
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia
| | - Jared Baxter
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Michael Hassall
- Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, QLD, 4350, Australia
| | - Adrian Hathorn
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia
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20
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Boyles RE, Brenton ZW, Kresovich S. Genetic and genomic resources of sorghum to connect genotype with phenotype in contrasting environments. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:19-39. [PMID: 30260043 DOI: 10.1111/tpj.14113] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/30/2018] [Accepted: 09/03/2018] [Indexed: 05/10/2023]
Abstract
With the recent development of genomic resources and high-throughput phenotyping platforms, the 21st century is primed for major breakthroughs in the discovery, understanding and utilization of plant genetic variation. Significant advances in agriculture remain at the forefront to increase crop production and quality to satisfy the global food demand in a changing climate all while reducing the environmental impacts of the world's food production. Sorghum, a resilient C4 grain and grass important for food and energy production, is being extensively dissected genetically and phenomically to help connect the relationship between genetic and phenotypic variation. Unlike genetically modified crops such as corn or soybean, sorghum improvement has relied heavily on public research; thus, many of the genetic resources serve a dual purpose for both academic and commercial pursuits. Genetic and genomic resources not only provide the foundation to identify and understand the genes underlying variation, but also serve as novel sources of genetic and phenotypic diversity in plant breeding programs. To better disseminate the collective information of this community, we discuss: (i) the genomic resources of sorghum that are at the disposal of the research community; (ii) the suite of sorghum traits as potential targets for increasing productivity in contrasting environments; and (iii) the prospective approaches and technologies that will help to dissect the genotype-phenotype relationship as well as those that will apply foundational knowledge for sorghum improvement.
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Affiliation(s)
- Richard E Boyles
- Pee Dee Research and Education Center, Clemson University, 2200 Pocket Rd, Florence, SC, 29506, USA
- Advanced Plant Technology Program, Clemson University, 105 Collings St, Clemson, SC, 29634, USA
| | - Zachary W Brenton
- Advanced Plant Technology Program, Clemson University, 105 Collings St, Clemson, SC, 29634, USA
- Department of Plant and Environment Sciences, Clemson University, 171 Poole Agricultural Center, Clemson, SC, 29634, USA
| | - Stephen Kresovich
- Advanced Plant Technology Program, Clemson University, 105 Collings St, Clemson, SC, 29634, USA
- Department of Plant and Environment Sciences, Clemson University, 171 Poole Agricultural Center, Clemson, SC, 29634, USA
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Dinglasan EG, Singh D, Shankar M, Afanasenko O, Platz G, Godwin ID, Voss-Fels KP, Hickey LT. Discovering new alleles for yellow spot resistance in the Vavilov wheat collection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:149-162. [PMID: 30327845 DOI: 10.1007/s00122-018-3204-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 10/09/2018] [Indexed: 06/08/2023]
Abstract
GWAS detected 11 yellow spot resistance QTL in the Vavilov wheat collection. Promising adult-plant resistance loci could provide a sustainable genetic solution to yellow spot in modern wheat varieties. Yellow spot, caused by the fungal pathogen Pyrenophora tritici-repentis (Ptr), is the most economically damaging foliar disease of wheat in Australia. Genetic resistance is considered to be the most sustainable means for disease management, yet the genomic regions underpinning resistance to Ptr, particularly adult-plant resistance (APR), remain vastly unknown. In this study, we report results of a genome-wide association study using 295 accessions from the Vavilov wheat collection which were extensively tested for response to Ptr infections in glasshouse and field trials at both seedling an adult growth stages. Combining phenotypic datasets from multiple experiments in Australia and Russia with 25,286 genome-wide, high-quality DArTseq markers, we detected a total of 11 QTL, of which 5 were associated with seedling resistance, 3 with all-stage resistance, and 3 with APR. Interestingly, the novel APR QTL were effective even in the presence of host sensitivity gene Tsn1. These genomic regions could offer broad-spectrum yellow spot protection, not just to ToxA but also other pathogenicity or virulence factors. Vavilov wheat accessions carrying APR QTL combinations displayed enhanced levels of resistance highlighting the potential for QTL stacking through breeding. We propose that the APR genetic factors discovered in our study could be used to improve resistance levels in modern wheat varieties and contribute to the sustainable control of yellow spot.
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Affiliation(s)
- Eric G Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Dharmendra Singh
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Manisha Shankar
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
- School of Agriculture and Environment, University of Western Australia, Crawley, WA, Australia
| | - Olga Afanasenko
- Department of Plant Resistance to Diseases, All-Russian Research Institute of Plant Protection, St. Petersburg, Russia
| | - Greg Platz
- Department of Agriculture and Fisheries, Hermitage Research Facility (HRF), Warwick, QLD, Australia
| | - Ian D Godwin
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia.
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia.
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22
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Zhou F, Liu Y, Liang C, Wang W, Li C, Guo Y, Ma J, Yu Y, Fan L, Yao Y, Zhao D, Liu X, Huang X. Construction of a high-density genetic linkage map and QTL mapping of oleic acid content and three agronomic traits in sunflower ( Helianthus annuus L.) using specific-locus amplified fragment sequencing (SLAF-seq). BREEDING SCIENCE 2018; 68:596-605. [PMID: 30697121 PMCID: PMC6345229 DOI: 10.1270/jsbbs.18051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/18/2018] [Indexed: 05/19/2023]
Abstract
High-density genetic linkage maps are particularly important for quantitative trait loci (QTL) mapping, genome assembly, and marker-assisted selection (MAS) in plants. In this study, a high-density genetic linkage map of sunflower (Helianthus annuus L.) was constructed using an F2 population generated from a cross between Helianthus annuus L. '86-1' and 'L-1-OL-1' via specific-locus amplified fragment sequencing (SLAF-seq). After sequence preprocessing, 530.50 M reads (105.60 Gb) were obtained that contained a total of 343,197 SLAFs, of which 39,589 were polymorphic. Of the polymorphic SLAFs, 6,136 were organized into a linkage map consisting of 17 linkage groups (LGs) spanning 2,221.86 cM, with an average genetic distance of 0.36 cM between SLAFs. Based on this high-density genetic map, QTL analysis was performed that focused on four sunflower phenotypic traits: oleic acid content (OAC), plant height (PH), head diameter (HD), and stem diameter (SD). Subsequently, for these four traits eight QTLs were detected that will likely be useful for increasing our understanding of genetic factors underlying these traits and for use in marker-assisted selection (MAS) for future sunflower breeding.
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Affiliation(s)
- Fei Zhou
- College of Life Science, Northeast Forestry University,
Harbin, 150040,
China
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Yan Liu
- College of Life Science, Northeast Forestry University,
Harbin, 150040,
China
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Chunbo Liang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Wenjun Wang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Cen Li
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Yongli Guo
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Jun Ma
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Ying Yu
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Lijuan Fan
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Yubo Yao
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Dongsheng Zhao
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Xuemei Liu
- College of Life Science, Northeast Forestry University,
Harbin, 150040,
China
| | - Xutang Huang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
- Corresponding author (e-mail: )
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Kante M, Rattunde HFW, Nébié B, Weltzien E, Haussmann BIG, Leiser WL. QTL mapping and validation of fertility restoration in West African sorghum A 1 cytoplasm and identification of a potential causative mutation for Rf 2. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2397-2412. [PMID: 30132022 PMCID: PMC6208960 DOI: 10.1007/s00122-018-3161-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 08/03/2018] [Indexed: 06/08/2023]
Abstract
Key message Major A 1 cytoplasm fertility restoration loci, Rf 2 and Rf 5 , were found in the West African sorghum. A potential causative mutation for Rf 2 was identified. KASP markers were validated on independent material. To accelerate the identification and development of hybrid parental lines in West African (WA) sorghum, this study aimed to understand the genetics underlying the fertility restoration (Rf) in WA A1 cytoplasmic male sterility system and to develop markers for a routine use in WA breeding programs. We genotyped by sequencing three F2 populations to map the Rf quantitative trait loci (QTL), validated the molecular KASP markers developed from those QTL in two F2:3 populations, and assessed the most promising markers on a set of 95 R- and B-lines from WA breeding programs. Seven QTL were found across the three F2 populations. On chromosome SBI-05, we found a major fertility restorer locus (Rf5) for two populations with the same male parent, explaining 19 and 14% of the phenotypic variation in either population. Minor QTL were detected in these two populations on chromosomes SBI-02, SBI-03, SBI-04 and SBI-10. In the third population, we identified one major fertility restorer locus on chromosome SBI-02, Rf2, explaining 31% of the phenotypic variation. Pentatricopeptide repeat genes in the Rf2 QTL region were sequenced, and we detected in Sobic.002G057050 a missense mutation in the first exon, explaining 81% of the phenotypic variation in a F2:3 population and clearly separating B- from R-lines. The KASP marker developed from this mutation stands as a promising tool for routine use in WA breeding programs.
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Affiliation(s)
- Moctar Kante
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | | | - Baloua Nébié
- International Crops Research Institute for the Semi-Arid Tropics, BP 320, Bamako, Mali
| | - Eva Weltzien
- University of Wisconsin-Madison, Madison, WI, USA
| | - Bettina I G Haussmann
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | - Willmar L Leiser
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599, Stuttgart, Germany.
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24
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Casto AL, McKinley BA, Yu KMJ, Rooney WL, Mullet JE. Sorghum stem aerenchyma formation is regulated by SbNAC_D during internode development. PLANT DIRECT 2018; 2:e00085. [PMID: 31245693 PMCID: PMC6508845 DOI: 10.1002/pld3.85] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 09/12/2018] [Indexed: 05/10/2023]
Abstract
Sorghum bicolor is a drought-resilient C4 grass used for production of grain, forage, sugar, and biomass. Sorghum genotypes capable of accumulating high levels of stem sucrose have solid stems that contain low levels of aerenchyma. The D-locus on SBI06 modulates the extent of aerenchyma formation in sorghum stems and leaf midribs. A QTL aligned with this locus was identified and fine-mapped in populations derived from BTx623*IS320c, BTx623*R07007, and BTx623*Standard broomcorn. Analysis of coding polymorphisms in the fine-mapped D-locus showed that genotypes that accumulate low levels of aerenchyma encode a truncated NAC transcription factor (Sobic.006G147400, SbNAC_d1), whereas parental lines that accumulate higher levels of stem aerenchyma encode full-length NAC TFs (SbNAC-D). During vegetative stem development, aerenchyma levels are low in nonelongated stem internodes, internode growing zones, and nodes. Aerenchyma levels increase in recently elongated internodes starting at the top of the internode near the center of the stem. SbNAC_D was expressed at low levels in nonelongated internodes and internode growing zones and at higher levels in regions of stem internodes that form aerenchyma. SbXCP1, a gene encoding a cysteine protease involved in programmed cell death, was induced in SbNAC_D genotypes in parallel with aerenchyma formation in sorghum stems but not in SbNAC_d1 genotypes. Several sweet sorghum genotypes encode the recessive SbNAC_d1 allele and have low levels of stem aerenchyma. Based on these results, we propose that SbNAC_D is the D-gene identified by Hilton (1916) and that allelic variation in SbNAC_D modulates the extent of aerenchyma formation in sorghum stems.
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Affiliation(s)
- Anna L. Casto
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexas
- Molecular and Environmental Plant Sciences Graduate ProgramTexas A&M UniversityCollege StationTexas
| | - Brian A. McKinley
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexas
| | - Ka Man Jasmine Yu
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexas
- Biochemistry and Biophysics Graduate ProgramTexas A&M UniversityCollege StationTexas
| | - William L. Rooney
- Department of Soil and Crop SciencesTexas A&M UniversityCollege StationTexas
| | - John E. Mullet
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexas
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Yan S, Wang L, Zhao L, Wang H, Wang D. Evaluation of Genetic Variation among Sorghum Varieties from Southwest China via Genome Resequencing. THE PLANT GENOME 2018; 11:170098. [PMID: 30512039 DOI: 10.3835/plantgenome2017.11.0098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Little is known regarding genomic variation among glutinous sorghum [ (L.) Moench] varieties grown in southwest China, which are primarily used to brew the popular Jiang-flavor liquor. This study evaluated genomic variation among six representative sorghum accessions via whole-genome resequencing. The evaluation revealed 2365,363 single-nucleotide polymorphisms (SNPs), 394,365 insertions and deletions, and 47,567 copy number variations among the six genomes. Chromosomes 5 and 10 showed relatively high SNP densities, whereas whole-genome diversity in this population was low. In addition, some chromosomal loci exhibited obvious selection during the breeding process. Sorghum accessions from southwest China formed an elite germplasm population compared with the findings of other geographic populations, and the elite variety 'Hongyingzi' contained 79 unique genes primarily involved in basic metabolism. The six sorghum lines contained a large number of high-confidence genes, with Hongyingzi in particular possessing 104 unique genes. These findings advance our understanding of domestication of the sorghum genome, and Chinese sorghum accessions will be valuable resources for further research and breeding improvements.
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26
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Borzęcka E, Hawliczek-Strulak A, Bolibok L, Gawroński P, Tofil K, Milczarski P, Stojałowski S, Myśków B, Targońska-Karasek M, Grądzielewska A, Smolik M, Kilian A, Bolibok-Brągoszewska H. Effective BAC clone anchoring with genotyping-by-sequencing and Diversity Arrays Technology in a large genome cereal rye. Sci Rep 2018; 8:8428. [PMID: 29849048 PMCID: PMC5976670 DOI: 10.1038/s41598-018-26541-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/16/2018] [Indexed: 11/09/2022] Open
Abstract
Identification of bacterial artificial chromosome (BAC) clones containing specific sequences is a prerequisite for many applications, such as physical map anchoring or gene cloning. Existing BAC library screening strategies are either low-throughput or require a considerable initial input of resources for platform establishment. We describe a high-throughput, reliable, and cost-effective BAC library screening approach deploying genotyping platforms which are independent from the availability of sequence information: a genotyping-by-sequencing (GBS) method DArTSeq and the microarray-based Diversity Arrays Technology (DArT). The performance of these methods was tested in a very large and complex rye genome. The DArTseq approach delivered superior results: a several fold higher efficiency of addressing genetic markers to BAC clones and anchoring of BAC clones to genetic map and also a higher reliability. Considering the sequence independence of the platform, the DArTseq-based library screening can be proposed as an attractive method to speed up genomics research in resource poor species.
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Affiliation(s)
- Ewa Borzęcka
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Anna Hawliczek-Strulak
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Leszek Bolibok
- Department of Silviculture, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Katarzyna Tofil
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Paweł Milczarski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Stefan Stojałowski
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Beata Myśków
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Małgorzata Targońska-Karasek
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Agnieszka Grądzielewska
- Institute of Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland
| | - Miłosz Smolik
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Slowackiego 17, 71-434, Szczecin, Poland
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Kirinari st, ACT 2617, Bruce, Australia
| | - Hanna Bolibok-Brągoszewska
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences - SGGW, Nowoursynowska 159, 02-776, Warsaw, Poland.
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Kumar S, Hash CT, Nepolean T, Mahendrakar MD, Satyavathi CT, Singh G, Rathore A, Yadav RS, Gupta R, Srivastava RK. Mapping Grain Iron and Zinc Content Quantitative Trait Loci in an Iniadi-Derived Immortal Population of Pearl Millet. Genes (Basel) 2018; 9:E248. [PMID: 29751669 PMCID: PMC5977188 DOI: 10.3390/genes9050248] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 04/23/2018] [Accepted: 05/01/2018] [Indexed: 11/27/2022] Open
Abstract
Pearl millet is a climate-resilient nutritious crop requiring low inputs and is capable of giving economic returns in marginal agro-ecologies. In this study, we report large-effect iron (Fe) and zinc (Zn) content quantitative trait loci (QTLs) using diversity array technology (DArT) and simple sequence repeats (SSRs) markers to generate a genetic linkage map using 317 recombinant inbred line (RIL) population derived from the (ICMS 8511-S1-17-2-1-1-B-P03 × AIMP 92901-S1-183-2-2-B-08) cross. The base map [seven linkage groups (LGs)] of 196 loci was 964.2 cM in length (Haldane). AIMP 92901-S1-183-2-2-B-08 is an Iniadi line with high grain Fe and Zn, tracing its origin to the Togolese Republic, West Africa. The content of grain Fe in the RIL population ranged between 20 and 131 ppm (parts per million), and that of Zn from 18 to 110 ppm. QTL analysis revealed a large number of QTLs for high grain iron (Fe) and zinc (Zn) content. A total of 19 QTLs for Fe and Zn were detected, of which 11 were for Fe and eight were for Zn. The portion of the observed phenotypic variance explained by different QTLs for grain Fe and Zn content varied from 9.0 to 31.9% (cumulative 74%) and from 9.4 to 30.4% (cumulative 65%), respectively. Three large-effect QTLs for both minerals were co-mapped in this population, one on LG1 and two on LG7. The favorable QTL alleles of both mineral micronutrients were contributed by the male parent (AIMP 92901-deriv-08). Three putative epistasis interactions were observed for Fe content, while a single digenic interaction was found for Zn content. The reported QTLs may be useful in marker-assisted selection (MAS) programs, in genomic selection (GS) breeding pipelines for seed and restorer parents, and in population improvement programs for pearl millet.
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Affiliation(s)
- Sushil Kumar
- Plant Biotechnology Centre, SK Rajasthan Agricultural University, Bikaner 334006, India.
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India.
- Centre of Excellence in Biotechnology, Anand Agricultural University, Anand, Gujarat 388110, India.
| | - Charles Tom Hash
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Niamey 8001, Niger.
| | | | - Mahesh D Mahendrakar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India.
| | | | - Govind Singh
- Plant Biotechnology Centre, SK Rajasthan Agricultural University, Bikaner 334006, India.
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India.
| | - Rattan S Yadav
- Crop Genetics, Genomics and Breeding Division, Aberystwyth University, Aberystwyth SY23, UK.
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India.
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana 502324, India.
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28
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Hu XH, Zhang SZ, Miao HR, Cui FG, Shen Y, Yang WQ, Xu TT, Chen N, Chi XY, Zhang ZM, Chen J. High-Density Genetic Map Construction and Identification of QTLs Controlling Oleic and Linoleic Acid in Peanut using SLAF-seq and SSRs. Sci Rep 2018; 8:5479. [PMID: 29615772 PMCID: PMC5883025 DOI: 10.1038/s41598-018-23873-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 03/20/2018] [Indexed: 11/08/2022] Open
Abstract
The cultivated peanut, A. hypogaea L., is an important oil and food crop globally.High-density genetic linkage mapping is a valuable and effective method for exploring complex quantitative traits. In this context, a recombinant inbred line (RIL) of 146 lines was developed by crossing Huayu28 and P76. We developed 433,679 high-quality SLAFs, of which 29,075 were polymorphic. 4,817 SLAFs were encoded and grouped into different segregation patterns. A high-resolution genetic map containing 2,334 markers (68 SSRs and 2,266 SNPs) on 20 linkage groups (LGs) spanning 2586.37 cM was constructed for peanut. The average distance between adjacent markers was 2.25 cM. Based on phenotyping in seven environments, QTLs for oleic acid (C18:1), linoleic acid (C18:2) and the ratio of oleic acid to linoleic acid (O/L) were identified and positioned on linkage groups A03, A04, A09, B09 and B10. Marker2575339 and Marker2379598 in B09 were associated with C18:1, C18:2 and O/L in seven environments, Marker4391589 and Marker4463600 in A09 were associated with C18:1, C18:2 and O/L in six environments. This map exhibits high resolution and accuracy, which will facilitate QTL discovery for essential agronomic traits in peanut.
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Affiliation(s)
- X H Hu
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - S Z Zhang
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - H R Miao
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - F G Cui
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - Y Shen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - W Q Yang
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - T T Xu
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - N Chen
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - X Y Chi
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - Z M Zhang
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - J Chen
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China.
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29
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Ates D, Aldemir S, Alsaleh A, Erdogmus S, Nemli S, Kahriman A, Ozkan H, Vandenberg A, Tanyolac B. A consensus linkage map of lentil based on DArT markers from three RIL mapping populations. PLoS One 2018; 13:e0191375. [PMID: 29351563 PMCID: PMC5774769 DOI: 10.1371/journal.pone.0191375] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 01/03/2018] [Indexed: 12/21/2022] Open
Abstract
Background Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. Materials and methods A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including “CDC Redberry” x “ILL7502” (LR8), “ILL8006” x “CDC Milestone” (LR11) and “PI320937” x “Eston” (LR39). Results The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. Conclusion This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.
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Affiliation(s)
- Duygu Ates
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey
| | - Secil Aldemir
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey
| | - Ahmad Alsaleh
- Department of Field Crops, Faculty of Agriculture, Cukurova University, Adana, Turkey
| | - Semih Erdogmus
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey
| | - Seda Nemli
- Department of Bieoengineering and Genetics, Gumushane University, Gumushane, Turkey
| | - Abdullah Kahriman
- Department of Field Crops, Faculty of Agriculture, Harran University, Sanlı Urfa, Turkey
| | - Hakan Ozkan
- Department of Field Crops, Faculty of Agriculture, Cukurova University, Adana, Turkey
| | - Albert Vandenberg
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Bahattin Tanyolac
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey
- * E-mail:
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30
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High density SNP and DArT-based genetic linkage maps of two closely related oil palm populations. J Appl Genet 2017; 59:23-34. [PMID: 29214520 DOI: 10.1007/s13353-017-0420-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/16/2017] [Accepted: 11/23/2017] [Indexed: 12/22/2022]
Abstract
Oil palm (Elaeis guineensis Jacq.) is an outbreeding perennial tree crop with long breeding cycles, typically 12 years. Molecular marker technologies can greatly improve the breeding efficiency of oil palm. This study reports the first use of the DArTseq platform to genotype two closely related self-pollinated oil palm populations, namely AA0768 and AA0769 with 48 and 58 progeny respectively. Genetic maps were constructed using the DArT and SNP markers generated in combination with anchor SSR markers. Both maps consisted of 16 major independent linkage groups (2n = 2× = 32) with 1399 and 1466 mapped markers for the AA0768 and AA0769 populations, respectively, including the morphological trait "shell-thickness" (Sh). The map lengths were 1873.7 and 1720.6 cM with an average marker density of 1.34 and 1.17 cM, respectively. The integrated map was 1803.1 cM long with 2066 mapped markers and average marker density of 0.87 cM. A total of 82% of the DArTseq marker sequence tags identified a single site in the published genome sequence, suggesting preferential targeting of gene-rich regions by DArTseq markers. Map integration of higher density focused around the Sh region identified closely linked markers to the Sh, with D.15322 marker 0.24 cM away from the morphological trait and 5071 bp from the transcriptional start of the published SHELL gene. Identification of the Sh marker demonstrates the robustness of using the DArTseq platform to generate high density genetic maps of oil palm with good genome coverage. Both genetic maps and integrated maps will be useful for quantitative trait loci analysis of important yield traits as well as potentially assisting the anchoring of genetic maps to genomic sequences.
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31
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Ziems LA, Franckowiak JD, Platz GJ, Mace ES, Park RF, Singh D, Jordan DR, Hickey LT. Investigating successive Australian barley breeding populations for stable resistance to leaf rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2463-2477. [PMID: 28836114 DOI: 10.1007/s00122-017-2970-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/14/2017] [Indexed: 06/07/2023]
Abstract
Genome-wide association studies of barley breeding populations identified candidate minor genes for pairing with the adult plant resistance gene Rph20 to provide stable leaf rust resistance across environments. Stable resistance to barley leaf rust (BLR, caused by Puccinia hordei) was evaluated across environments in barley breeding populations (BPs). To identify genomic regions that can be combined with Rph20 to improve adult plant resistance (APR), two BPs genotyped with the Diversity Arrays Technology genotyping-by-sequencing platform (DArT-seq) were examined for reaction to BLR at both seedling and adult growth stages in Australian environments. An integrated consensus map comprising both first- and second-generation DArT platforms was used to integrate QTL information across two additional BPs, providing a total of four interrelated BPs and 15 phenotypic data sets. This enabled identification of key loci underpinning BLR resistance. The APR gene Rph20 was the only active resistance region consistently detected across BPs. Of the QTL identified, RphQ27 on chromosome 6HL was considered the best candidate for pairing with Rph20. RphQ27 did not align or share proximity with known genes and was detected in three of the four BPs. The combination of RphQ27 and Rph20 was of low frequency in the breeding material; however, strong resistance responses were observed for the lines carrying this pairing. This suggests that the candidate minor gene RphQ27 can interact additively with Rph20 to provide stable resistance to BLR across diverse environments.
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Affiliation(s)
- L A Ziems
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - J D Franckowiak
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, 55108, USA
| | - G J Platz
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - E S Mace
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - R F Park
- The University of Sydney, Plant Breeding Institute, Narellan, NSW, 2567, Australia
| | - D Singh
- The University of Sydney, Plant Breeding Institute, Narellan, NSW, 2567, Australia
| | - D R Jordan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - L T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, 4072, Australia
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32
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Increased Power To Dissect Adaptive Traits in Global Sorghum Diversity Using a Nested Association Mapping Population. Genetics 2017; 206:573-585. [PMID: 28592497 PMCID: PMC5499173 DOI: 10.1534/genetics.116.198499] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/09/2017] [Indexed: 11/18/2022] Open
Abstract
Adaptation of domesticated species to diverse agroclimatic regions has led to abundant trait diversity. However, the resulting population structure and genetic heterogeneity confounds association mapping of adaptive traits. To address this challenge in sorghum [Sorghum bicolor (L.) Moench]-a widely adapted cereal crop-we developed a nested association mapping (NAM) population using 10 diverse global lines crossed with an elite reference line RTx430. We characterized the population of 2214 recombinant inbred lines at 90,000 SNPs using genotyping-by-sequencing. The population captures ∼70% of known global SNP variation in sorghum, and 57,411 recombination events. Notably, recombination events were four- to fivefold enriched in coding sequences and 5' untranslated regions of genes. To test the power of the NAM population for trait dissection, we conducted joint linkage mapping for two major adaptive traits, flowering time and plant height. We precisely mapped several known genes for these two traits, and identified several additional QTL. Considering all SNPs simultaneously, genetic variation accounted for 65% of flowering time variance and 75% of plant height variance. Further, we directly compared NAM to genome-wide association mapping (using panels of the same size) and found that flowering time and plant height QTL were more consistently identified with the NAM population. Finally, for simulated QTL under strong selection in diversity panels, the power of QTL detection was up to three times greater for NAM vs. association mapping with a diverse panel. These findings validate the NAM resource for trait mapping in sorghum, and demonstrate the value of NAM for dissection of adaptive traits.
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33
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Gelli M, Konda AR, Liu K, Zhang C, Clemente TE, Holding DR, Dweikat IM. Validation of QTL mapping and transcriptome profiling for identification of candidate genes associated with nitrogen stress tolerance in sorghum. BMC PLANT BIOLOGY 2017; 17:123. [PMID: 28697783 PMCID: PMC5505042 DOI: 10.1186/s12870-017-1064-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 06/25/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Quantitative trait loci (QTLs) detected in one mapping population may not be detected in other mapping populations at all the time. Therefore, before being used for marker assisted breeding, QTLs need to be validated in different environments and/or genetic backgrounds to rule out statistical anomalies. In this regard, we mapped the QTLs controlling various agronomic traits in a recombinant inbred line (RIL) population in response to Nitrogen (N) stress and validated these with the reported QTLs in our earlier study to find the stable and consistent QTLs across populations. Also, with Illumina RNA-sequencing we checked the differential expression of gene (DEG) transcripts between parents and pools of RILs with high and low nitrogen use efficiency (NUE) and overlaid these DEGs on to the common validated QTLs to find candidate genes associated with N-stress tolerance in sorghum. RESULTS An F7 RIL population derived from a cross between CK60 (N-stress sensitive) and San Chi San (N-stress tolerant) inbred sorghum lines was used to map QTLs for 11 agronomic traits tested under different N-levels. Composite interval mapping analysis detected a total of 32 QTLs for 11 agronomic traits. Validation of these QTLs revealed that of the detected, nine QTLs from this population were consistent with the reported QTLs in earlier study using CK60/China17 RIL population. The validated QTLs were located on chromosomes 1, 6, 7, 8, and 9. In addition, root transcriptomic profiling detected 55 and 20 differentially expressed gene (DEG) transcripts between parents and pools of RILs with high and low NUE respectively. Also, overlay of these DEG transcripts on to the validated QTLs found candidate genes transcripts for NUE and also showed the expected differential expression. For example, DEG transcripts encoding Lysine histidine transporter 1 (LHT1) had abundant expression in San Chi San and the tolerant RIL pool, whereas DEG transcripts encoding seed storage albumin, transcription factor IIIC (TFIIIC) and dwarfing gene (DW2) encoding multidrug resistance-associated protein-9 homolog showed abundant expression in CK60 parent, similar to earlier study. CONCLUSIONS The validated QTLs among different mapping populations would be the most reliable and stable QTLs across germplasm. The DEG transcripts found in the validated QTL regions will serve as future candidate genes for enhancing NUE in sorghum using molecular approaches.
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Affiliation(s)
- Malleswari Gelli
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
| | - Anji Reddy Konda
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
| | - Kan Liu
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA
| | - Thomas E Clemente
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
| | - David R Holding
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA
| | - Ismail M Dweikat
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
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Ziems LA, Hickey LT, Platz GJ, Franckowiak JD, Dracatos PM, Singh D, Park RF. Characterization of Rph24: A Gene Conferring Adult Plant Resistance to Puccinia hordei in Barley. PHYTOPATHOLOGY 2017; 107:834-841. [PMID: 28430019 DOI: 10.1094/phyto-08-16-0295-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We identified Rph24 as a locus in barley (Hordeum vulgare L.) controlling adult plant resistance (APR) to leaf rust, caused by Puccinia hordei. The locus was previously reported as a quantitative trait locus in barley line ND24260-1 and named qRphND. We crossed ND24260-1 to the leaf-rust-susceptible standard Gus and determined inheritance patterns in the progeny. For the comparative marker frequency analysis (MFA), resistant and susceptible tails of the F2 were genotyped with Diversity Arrays Technology genotyping-by-sequencing (DArT-Seq) markers. The Rph24 locus was positioned at 55.5 centimorgans on chromosome 6H on the DArT-Seq consensus map. Evaluation of F2:3 families confirmed that a single locus from ND24260-1 conferred partial resistance. The haploblock strongly associated with the Rph24 locus was used to estimate the allele frequency in a collection of 282 international barley cultivars. Rph24 was frequently paired with APR locus Rph20 in cultivars displaying high levels of APR to leaf rust. The markers identified in this study for Rph24 should be useful for marker-assisted selection.
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Affiliation(s)
- Laura A Ziems
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Lee T Hickey
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Gregory J Platz
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Jerome D Franckowiak
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Peter M Dracatos
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Davinder Singh
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
| | - Robert F Park
- First and second authors: The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St. Lucia, QLD 4072, Australia; third author: Department of Agriculture and Fisheries, Hermitage Research Facility, 604 Yangan Rd, Warwick, QLD 4370, Australia; fourth author: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul 55108; and fifth and sixth authors: The University of Sydney, Plant Breeding Institute Cobbitty, Private Bag 4011, Narellan, NSW 2167, Australia
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Mathur S, Umakanth AV, Tonapi VA, Sharma R, Sharma MK. Sweet sorghum as biofuel feedstock: recent advances and available resources. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:146. [PMID: 28603553 PMCID: PMC5465577 DOI: 10.1186/s13068-017-0834-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/30/2017] [Indexed: 05/08/2023]
Abstract
Sweet sorghum is a promising target for biofuel production. It is a C4 crop with low input requirements and accumulates high levels of sugars in its stalks. However, large-scale planting on marginal lands would require improved varieties with optimized biofuel-related traits and tolerance to biotic and abiotic stresses. Considering this, many studies have been carried out to generate genetic and genomic resources for sweet sorghum. In this review, we discuss various attributes of sweet sorghum that make it an ideal candidate for biofuel feedstock, and provide an overview of genetic diversity, tools, and resources available for engineering and/or marker-assisting breeding of sweet sorghum. Finally, the progress made so far, in identification of genes/quantitative trait loci (QTLs) important for agronomic traits and ongoing molecular breeding efforts to generate improved varieties, has been discussed.
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Affiliation(s)
- Supriya Mathur
- Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - A. V. Umakanth
- Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - V. A. Tonapi
- Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - Rita Sharma
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manoj K. Sharma
- Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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Genotyping-by-Sequencing Facilitates a High-Density Consensus Linkage Map for Aegilops umbellulata, a Wild Relative of Cultivated Wheat. G3-GENES GENOMES GENETICS 2017; 7:1551-1561. [PMID: 28364036 PMCID: PMC5427507 DOI: 10.1534/g3.117.039966] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
High-density genetic maps are useful to precisely localize QTL or genes that might be used to improve traits of nutritional and/or economical importance in crops. However, high-density genetic maps are lacking for most wild relatives of crop species, including wheat. Aegilops umbellulata is a wild relative of wheat known for its potential as a source of biotic and abiotic stress resistance genes. In this work, we have developed a framework consensus genetic map using two biparental populations derived from accessions PI 298905, PI 542369, PI 5422375, and PI 554395. The framework map comprised 3009 genotype-by-sequence SNPs with a total map size of 948.72 cM. On average, there were three SNPs per centimorgan for each chromosome. Chromosome 1U was the shortest (66.5 cM), with only 81 SNPs, whereas the remaining chromosomes had between 391 and 591 SNP markers. A total of 2395 unmapped SNPs were added to the linkage maps through a recombination frequency approach, and increased the number of SNPs placed on the consensus map to a total of 5404 markers. Segregation distortion was disproportionally high for chromosome 1U for both populations used to construct component linkage maps, and thus segregation distortion could be one of the probable reasons for the exceptionally reduced linkage size for chromosome 1U. From comparative analysis, Ae. umbellulata chromosomes except 4U showed moderate to strong collinearity with corresponding homeologous chromosomes of hexaploid wheat and barley. The present consensus map may serve as a reference map in QTL mapping and validation projects, and also in genome assembly to develop a reference genome sequence for Ae. umbellulata.
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Ji G, Zhang Q, Du R, Lv P, Ma X, Fan S, Li S, Hou S, Han Y, Liu G. Construction of a high-density genetic map using specific-locus amplified fragments in sorghum. BMC Genomics 2017; 18:51. [PMID: 28061813 PMCID: PMC5219666 DOI: 10.1186/s12864-016-3430-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/16/2016] [Indexed: 02/13/2023] Open
Abstract
BACKGROUND Sorghum is mainly used as a human food and beverage source, playing an important role in the production of ethanol and other bio-industrial products. Thus it is regarded as a model crop for energy plants. Genetic map construction is the foundation for marker-assisted selection and gene cloning. So far several sorghum linkage maps have been reported using different kinds of molecular markers. However marker numbers and chromosome coverage are limited. As a result, it is difficult to get consistent results and the maps are hard to unify. In the present study, the genomes of 130 individuals consisting an F2 population together with their parents were surveyed using a high-throughput sequencing technique. A high-density linkage map was constructed using specific-locus amplified fragments (SLAF) markers. This map can provide information and serve as a reference for effective gene exploration, and for marker assisted-breeding program. RESULTS A high-throughput sequencing method was adopted to screen SLAF markers with 130 F2 individuals from a cross between a grain sorghum variety, J204, and a sweet sorghum variety, Keter. In the present study, 52,928 suitable SLAF markers out of 43,528,021 pair-end reads were chosen to conduct genetic map construction, 12.0% of which were polymorphic. Among the 6353 polymorphic SLAF markers, 5829 (91.8%) were successfully genotyped in the F2 mapping population. Finally 2246 SLAF markers were obtained to construct a high-density genetic linkage map. The total distance of linkage map covering all 10 chromosomes was 2158.1 cM. The largest gap on each chromosome was 10.2 cM on average. The proportion of gaps less than and/or equal to 5.0 cM was averagely 98.1%. The markers on each chromosome ranged from 123 (chromosome 9) to 315 (chromosome 4) with a mean value of 224.6, the distance between adjacent markers ranged from 0.6 (chromosome 10) to 1.3 cM (chromosome 9) with an average distance of only 0.98 cM. CONCLUSION A high density sorghum genetic map was constructed in this study. The total length was 2158.1 cM covering all 10 chromosomes with a total number of 2246 SLAF markers. The construction of this map can provide detailed information for accurate gene localization and cloning and application of marker-assisted breeding.
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Affiliation(s)
- Guisu Ji
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China
| | - Qingjiang Zhang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural & Forestry Sciences, Shijiazhuang, 050035, China
| | - Ruiheng Du
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China
| | - Peng Lv
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China
| | - Xue Ma
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China
| | - Shu Fan
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Suying Li
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China
| | - Shenglin Hou
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China
| | - Yucui Han
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agricultural & Forestry Sciences/Hebei Branch of China National Sorghum Improvement Center, Shijiazhuang, 050035, China.
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Gorthy S, Narasu L, Gaddameedi A, Sharma HC, Kotla A, Deshpande SP, Are AK. Introgression of Shoot Fly ( Atherigona soccata L. Moench) Resistance QTLs into Elite Post-rainy Season Sorghum Varieties Using Marker Assisted Backcrossing (MABC). FRONTIERS IN PLANT SCIENCE 2017; 8:1494. [PMID: 28919901 PMCID: PMC5585744 DOI: 10.3389/fpls.2017.01494] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/11/2017] [Indexed: 05/19/2023]
Abstract
Shoot fly (Atherigona soccata L. Moench) is a serious pest in sorghum production. Management of shoot fly using insecticides is expensive and environmentally un-safe. Developing host-plant resistance is the best method to manage shoot fly infestation. Number of component traits contribute for imparting shoot fly resistance in sorghum and molecular markers have been reported which were closely linked to QTLs controlling these component traits. In this study, three QTLs associated with shoot fly resistance were introgressed into elite cultivars Parbhani Moti (= SPV1411) and ICSB29004 using marker assisted backcrossing (MABC). Crosses were made between recurrent parents and the QTL donors viz., J2658, J2614, and J2714. The F1s after confirmation for QTL presence were backcrossed to recurrent parents and the resultant lines after two backcrosses were selfed thrice for advancement. The foreground selection was carried out in F1 and BCnF1 generations with 22 polymorphic markers. Forty-three evenly distributed simple sequence repeat markers in the sorghum genome were used in background selection to identify plants with higher recurrent parent genome recovery. By using two backcrosses and four rounds of selfing, six BC2F4 progenies were selected for ICSB29004 × J2658, five BC2F4 progenies were selected for ICSB29004 × J2714 and six BC2F4 progenies were selected for Parbhani Moti × J2614 crosses. Phenotyping of these lines led to the identification of two resistant lines for each QTL region present on chromosome SBI-01, SBI-07 and SBI-10 in ICSB 29004 and Parbhani Moti. All the introgression lines (ILs) showed better shoot fly resistance than the recurrent parents and their agronomic performance was the same or better than the recurrent parents. Further, the ILs had medium plant height, desirable maturity with high yield potential which makes them better candidates for commercialization. In the present study, MABC has successfully improved the shoot fly resistance in sorghum without a yield penalty. This is the first report on the use of MABC for improving shoot fly resistance in post-rainy season sorghum.
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Affiliation(s)
- Sunita Gorthy
- International Crops Research Institute for Semi-Arid TropicsHyderabad, India
- Department of Biotechnology, Jawaharlal Nehru Technological UniversityHyderabad, India
| | - Lakshmi Narasu
- Department of Biotechnology, Jawaharlal Nehru Technological UniversityHyderabad, India
| | - Anil Gaddameedi
- International Crops Research Institute for Semi-Arid TropicsHyderabad, India
| | - Hari C. Sharma
- International Crops Research Institute for Semi-Arid TropicsHyderabad, India
| | - Anuradha Kotla
- International Crops Research Institute for Semi-Arid TropicsHyderabad, India
| | | | - Ashok K. Are
- International Crops Research Institute for Semi-Arid TropicsHyderabad, India
- *Correspondence: Ashok K. Are,
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Abstract
New crops are gradually establishing along with cultivation systems to reduce reliance on depleting fossil fuel reserves and sustain better adaptation to climate change. These biological assets could be efficiently exploited as bioenergy feedstocks. Bioenergy crops are versatile renewable sources with the potential to alternatively contribute on a daily basis towards the coverage of modern society's energy demands. Biotechnology may facilitate the breeding of elite energy crop genotypes, better suited for bio-processing and subsequent use that will improve efficiency, further reduce costs, and enhance the environmental benefits of biofuels. Innovative molecular techniques may improve a broad range of important features including biomass yield, product quality and resistance to biotic factors like pests or microbial diseases or environmental cues such as drought, salinity, freezing injury or heat shock. The current review intends to assess the capacity of biotechnological applications to develop a beneficial bioenergy pipeline extending from feedstock development to sustainable biofuel production and provide examples of the current state of the art on future energy crops.
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40
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Recent Perspective of Next Generation Sequencing: Applications in Molecular Plant Biology and Crop Improvement. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s40011-016-0770-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Fracasso A, Trindade LM, Amaducci S. Drought stress tolerance strategies revealed by RNA-Seq in two sorghum genotypes with contrasting WUE. BMC PLANT BIOLOGY 2016; 16:115. [PMID: 27208977 PMCID: PMC4875703 DOI: 10.1186/s12870-016-0800-x] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/05/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND Drought stress is the major environmental stress that affects plant growth and productivity. It triggers a wide range of responses detectable at molecular, biochemical and physiological levels. At the molecular level the response to drought stress results in the differential expression of several metabolic pathways. For this reason, exploring the subtle differences in gene expression of drought sensitive and drought tolerant genotypes enables the identification of drought-related genes that could be used for selection of drought tolerance traits. Genome-wide RNA-Seq technology was used to compare the drought response of two sorghum genotypes characterized by contrasting water use efficiency. RESULTS The physiological measurements carried out confirmed the drought sensitivity of IS20351 and the drought tolerance of IS22330 genotypes, as previously studied. The expression of drought-related genes was more abundant in the drought sensitive genotype IS20351 compared to the tolerant genotype IS22330. Under drought stress Gene Ontology enrichment highlighted a massive increase in transcript abundance in the sensitive genotype IS20351 in "response to stress" and "abiotic stimulus", as well as for "oxidation-reduction reaction". "Antioxidant" and "secondary metabolism", "photosynthesis and carbon fixation process", "lipids" and "carbon metabolism" were the pathways most affected by drought in the sensitive genotype IS20351. In addition, genotype IS20351 showed a lower constitutive expression level of "secondary metabolic process" (GO:0019748) and "glutathione transferase activity" (GO:000004364) under well-watered conditions. CONCLUSIONS RNA-Seq analysis proved to be a very useful tool to explore differences between sensitive and tolerant sorghum genotypes. Transcriptomics analysis results supported all the physiological measurements and were essential to clarify the tolerance of the two genotypes studied. The connection between differential gene expression and physiological response to drought unequivocally revealed the drought tolerance of genotype IS22330 and the strategy adopted to cope with drought stress.
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Affiliation(s)
- Alessandra Fracasso
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122, Piacenza, Italy.
| | - Luisa M Trindade
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, 6708 PD, Wageningen, The Netherlands
| | - Stefano Amaducci
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122, Piacenza, Italy
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Fracasso A, Trindade L, Amaducci S. Drought tolerance strategies highlighted by two Sorghum bicolor races in a dry-down experiment. JOURNAL OF PLANT PHYSIOLOGY 2016; 190:1-14. [PMID: 26624226 DOI: 10.1016/j.jplph.2015.10.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/24/2015] [Accepted: 10/26/2015] [Indexed: 05/20/2023]
Abstract
Drought stress is the major environmental stress that affects more and more frequently plant growth and productivity due to the current climate change scenario. Unravelling the physiological mechanism underlying the response of plants to water stress and discover traits related to drought tolerance provide new and powerful tools for the selection in breeding programmes. Four genotypes of Sorghum bicolor (L.) Moench were screened in a dry-down experiment using different approaches to discover physiological and molecular indicators of drought tolerance. Different strategies were identified in response to drought among the four genotypes and the two Sorghum race allowing to state the tolerance of durra race compared to the caudatum one and, within the durra race, the drought tolerance of the genotype IS22330. It retained high biomass production and high tolerance index, it had a low threshold of fraction of transpirable soil water and high capacity to recover leaf apparatus after drought stress. Furthermore in this study, the expression levels of four genes highlighted that they could be used as proxy for drought tolerance. Dehdrine (DHN) could be used for screening drought tolerance both in durra and in caudatum races. NADP-Malic Enzyme, Carbonic Anhydrase (CA) and Plasma membrane Intrinsic Protein (PIP2-5), being up-regulated by drought stress only in durra race, have a more limited, though nonetheless useful application. In the tolerant durra genotype IS22330 in particular, the regulation of stomatal openings was strongly related to NADP-Malic Enzyme expression.
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Affiliation(s)
- Alessandra Fracasso
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy.
| | - Luisa Trindade
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, 6708 PD Wageningen, The Netherlands.
| | - Stefano Amaducci
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy.
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Gelli M, Mitchell SE, Liu K, Clemente TE, Weeks DP, Zhang C, Holding DR, Dweikat IM. Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum. BMC PLANT BIOLOGY 2016; 16:16. [PMID: 26759170 PMCID: PMC4710988 DOI: 10.1186/s12870-015-0696-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/21/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND Sorghum is an important C4 crop which relies on applied Nitrogen fertilizers (N) for optimal yields, of which substantial amounts are lost into the atmosphere. Understanding the genetic variation of sorghum in response to limited nitrogen supply is important for elucidating the underlying genetic mechanisms of nitrogen utilization. RESULTS A bi-parental mapping population consisting of 131 recombinant inbred lines (RILs) was used to map quantitative trait loci (QTLs) influencing different agronomic traits evaluated under normal N (100 kg.ha(-1) fertilizer) and low N (0 kg.ha(-1) fertilizer) conditions. A linkage map spanning 1614 cM was developed using 642 polymorphic single nucleotide polymorphisms (SNPs) detected in the population using Genotyping-By-Sequencing (GBS) technology. Composite interval mapping detected a total of 38 QTLs for 11 agronomic traits tested under different nitrogen levels. The phenotypic variation explained by individual QTL ranged from 6.2 to 50.8%. Illumina RNA sequencing data generated on seedling root tissues revealed 726 differentially expressed gene (DEG) transcripts between parents, of which 108 were mapped close to the QTL regions. CONCLUSIONS Co-localized regions affecting multiple traits were detected on chromosomes 1, 5, 6, 7 and 9. These potentially pleiotropic regions were coincident with the genomic regions of cloned QTLs, including genes associated with flowering time, Ma3 on chromosome 1 and Ma1 on chromosome 6, gene associated with plant height, Dw2 on chromosome 6. In these regions, RNA sequencing data showed differential expression of transcripts related to nitrogen metabolism (Ferredoxin-nitrate reductase), glycolysis (Phosphofructo-2-kinase), seed storage proteins, plant hormone metabolism and membrane transport. The differentially expressed transcripts underlying the pleiotropic QTL regions could be potential targets for improving sorghum performance under limited N fertilizer through marker assisted selection.
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Affiliation(s)
- Malleswari Gelli
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
| | - Sharon E Mitchell
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA.
- Institute of Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
| | - Kan Liu
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA.
- Institute of Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
| | - Thomas E Clemente
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
| | - Donald P Weeks
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA.
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA.
- Institute of Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
| | - David R Holding
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
| | - Ismail M Dweikat
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
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Satish L, Shilpha J, Pandian S, Rency AS, Rathinapriya P, Ceasar SA, Largia MJV, Kumar AA, Ramesh M. Analysis of genetic variation in sorghum (Sorghum bicolor (L.) Moench) genotypes with various agronomical traits using SPAR methods. Gene 2016; 576:581-5. [DOI: 10.1016/j.gene.2015.10.056] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 10/21/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
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Shen X, Liu ZQ, Mocoeur A, Xia Y, Jing HC. PAV markers in Sorghum bicolour: genome pattern, affected genes and pathways, and genetic linkage map construction. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:623-37. [PMID: 25634103 PMCID: PMC4361761 DOI: 10.1007/s00122-015-2458-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 01/06/2015] [Indexed: 05/23/2023]
Abstract
KEY MESSAGE 5,511 genic small-size PAVs in sorghum were identified and examined, including the pattern and the function enrichment of PAV genes. 325 PAV markers were developed to construct a genetic map. Presence/absence variants (PAVs) correlate closely to the phenotypic variation, by impacting plant genome sizes and the adaption to the environment. To shed more light on their genome-wide patterns, functions and the possibility of using them as molecular markers, we generated next generation genome sequencing data for four sorghum inbred lines and used associated bioinformatic pipelines to identify small-size PAVs (40-10 kb). Five thousand five hundreds and eleven genic PAVs (40-10 kb) were identified and found to affect 3,238 genes. These PAVs were mainly distributed on the sub-telomeric regions, but the highest proportions occurred in the vicinity of the centromeric regions. One of the prominent features of the PAVs is the high occurrence of long terminal repeats retrotransposons and DNA transposons. PAVs caused various alterations to gene structure, primarily including the coding sequence variants, intron variants, transcript ablation, and initiator codon changes. The genes affected by PAVs were significantly enriched in those involved in stress responses and protein modification. We used 325 PAVs polymorphic between two sorghum inbred lines Ji2731 and E-Tian, together with 49 SSR markers, and constructed a genetic map, which consisted of 10 linkage groups corresponding to the 10 chromosomes of sorghum and spanned 1,430.3 cM in length covering 97% of the physical genome. The resources reported here should be useful for genetic study and breeding of sorghum and related species.
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Affiliation(s)
- Xin Shen
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhi-Quan Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Anne Mocoeur
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
- Department of Plant and Environment, Faculty of Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Yan Xia
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China
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Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement. GENETICS RESEARCH INTERNATIONAL 2015; 2015:684321. [PMID: 25874133 PMCID: PMC4383144 DOI: 10.1155/2015/684321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/14/2014] [Accepted: 11/03/2014] [Indexed: 11/18/2022]
Abstract
The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away.
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Wang X, Mace ES, Platz GJ, Hunt CH, Hickey LT, Franckowiak JD, Jordan DR. Spot form of net blotch resistance in barley is under complex genetic control. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:489-99. [PMID: 25575837 DOI: 10.1007/s00122-014-2447-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 12/17/2014] [Indexed: 05/12/2023]
Abstract
Evaluation of resistance to Pyrenophora teres f. maculata in barley breeding populations via association mapping revealed a complex genetic architecture comprising a mixture of major and minor effect genes. In the search for stable resistance to spot form of net blotch (Pyrenophora teres f. maculata, SFNB), association mapping was conducted on four independent barley (Hordeum vulgare L.) breeding populations comprising a total of 898 unique elite breeding lines from the Northern Region Barley Breeding Program in Australia for discovery of quantitative trait loci (QTL) influencing resistance at seedling and adult plant growth stages. A total of 29 significant QTL were validated across multiple breeding populations, with 22 conferring resistance at both seedling and adult plant growth stages. The remaining 7 QTL conferred resistance at either seedling (2 QTL) or adult plant (5 QTL) growth stages only. These 29 QTL represented 24 unique genomic regions, of which five were found to co-locate with previously identified QTL for SFNB. The results indicated that SFNB resistance is controlled by a large number of QTL varying in effect size with large effects QTL on chromosome 7H. A large proportion of the QTL acted in the same direction for both seedling and adult responses, suggesting that phenotypic selection for SFNB resistance performed at either growth stage could achieve adequate levels of resistance. However, the accumulation of specific resistance alleles on several chromosomes must be considered in molecular breeding selection strategies.
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Affiliation(s)
- Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation, Hermitage Research Facility, The University of Queensland, Warwick, QLD, 4370, Australia
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Wang X, Mace E, Hunt C, Cruickshank A, Henzell R, Parkes H, Jordan D. Two distinct classes of QTL determine rust resistance in sorghum. BMC PLANT BIOLOGY 2014; 14:366. [PMID: 25551674 PMCID: PMC4335369 DOI: 10.1186/s12870-014-0366-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 12/05/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND Agriculture is facing enormous challenges to feed a growing population in the face of rapidly evolving pests and pathogens. The rusts, in particular, are a major pathogen of cereal crops with the potential to cause large reductions in yield. Improving stable disease resistance is an on-going major and challenging focus for many plant breeding programs, due to the rapidly evolving nature of the pathogen. Sorghum is a major summer cereal crop that is also a host for a rust pathogen Puccinia purpurea, which occurs in almost all sorghum growing areas of the world, causing direct and indirect yield losses in sorghum worldwide, however knowledge about its genetic control is still limited. In order to further investigate this issue, QTL and association mapping methods were implemented to study rust resistance in three bi-parental populations and an association mapping set of elite breeding lines in different environments. RESULTS In total, 64 significant or highly significant QTL and 21 suggestive rust resistance QTL were identified representing 55 unique genomic regions. Comparisons across populations within the current study and with rust QTL identified previously in both sorghum and maize revealed a high degree of correspondence in QTL location. Negative phenotypic correlations were observed between rust, maturity and height, indicating a trend for both early maturing and shorter genotypes to be more susceptible to rust. CONCLUSIONS The significant amount of QTL co-location across traits, in addition to the consistency in the direction of QTL allele effects, has provided evidence to support pleiotropic QTL action across rust, height, maturity and stay-green, supporting the role of carbon stress in susceptibility to rust. Classical rust resistance QTL regions that did not co-locate with height, maturity or stay-green QTL were found to be significantly enriched for the defence-related NBS-encoding gene family, in contrast to the lack of defence-related gene enrichment in multi-trait effect rust resistance QTL. The distinction of disease resistance QTL hot-spots, enriched with defence-related gene families from QTL which impact on development and partitioning, provides plant breeders with knowledge which will allow for fast-tracking varieties with both durable pathogen resistance and appropriate adaptive traits.
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Affiliation(s)
- Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, Australia.
| | - Emma Mace
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | - Colleen Hunt
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, Australia.
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | - Alan Cruickshank
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | - Robert Henzell
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | - Heidi Parkes
- Department of Agriculture, Fisheries & Forestry (DAFF), Stanthorpe, QLD, Australia.
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, Australia.
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High-resolution linkage map and chromosome-scale genome assembly for cassava (Manihot esculenta Crantz) from 10 populations. G3-GENES GENOMES GENETICS 2014; 5:133-44. [PMID: 25504737 PMCID: PMC4291464 DOI: 10.1534/g3.114.015008] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cassava (Manihot esculenta Crantz) is a major staple crop in Africa, Asia, and South America, and its starchy roots provide nourishment for 800 million people worldwide. Although native to South America, cassava was brought to Africa 400-500 years ago and is now widely cultivated across sub-Saharan Africa, but it is subject to biotic and abiotic stresses. To assist in the rapid identification of markers for pathogen resistance and crop traits, and to accelerate breeding programs, we generated a framework map for M. esculenta Crantz from reduced representation sequencing [genotyping-by-sequencing (GBS)]. The composite 2412-cM map integrates 10 biparental maps (comprising 3480 meioses) and organizes 22,403 genetic markers on 18 chromosomes, in agreement with the observed karyotype. We used the map to anchor 71.9% of the draft genome assembly and 90.7% of the predicted protein-coding genes. The chromosome-anchored genome sequence will be useful for breeding improvement by assisting in the rapid identification of markers linked to important traits, and in providing a framework for genomic selection-enhanced breeding of this important crop.
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Alam MM, Mace ES, van Oosterom EJ, Cruickshank A, Hunt CH, Hammer GL, Jordan DR. QTL analysis in multiple sorghum populations facilitates the dissection of the genetic and physiological control of tillering. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2253-66. [PMID: 25163934 DOI: 10.1007/s00122-014-2377-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 08/02/2014] [Indexed: 05/04/2023]
Abstract
A QTL model for the genetic control of tillering in sorghum is proposed, presenting new opportunities for sorghum breeders to select germplasm with tillering characteristics appropriate for their target environments. Tillering in sorghum can be associated with either the carbon supply-demand (S/D) balance of the plant or an intrinsic propensity to tiller (PTT). Knowledge of the genetic control of tillering could assist breeders in selecting germplasm with tillering characteristics appropriate for their target environments. The aims of this study were to identify QTL for tillering and component traits associated with the S/D balance or PTT, to develop a framework model for the genetic control of tillering in sorghum. Four mapping populations were grown in a number of experiments in south east Queensland, Australia. The QTL analysis suggested that the contribution of traits associated with either the S/D balance or PTT to the genotypic differences in tillering differed among populations. Thirty-four tillering QTL were identified across the populations, of which 15 were novel to this study. Additionally, half of the tillering QTL co-located with QTL for component traits. A comparison of tillering QTL and candidate gene locations identified numerous coincident QTL and gene locations across populations, including the identification of common non-synonymous SNPs in the parental genotypes of two mapping populations in a sorghum homologue of MAX1, a gene involved in the control of tiller bud outgrowth through the production of strigolactones. Combined with a framework for crop physiological processes that underpin genotypic differences in tillering, the co-location of QTL for tillering and component traits and candidate genes allowed the development of a framework QTL model for the genetic control of tillering in sorghum.
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Affiliation(s)
- M M Alam
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
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