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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. Theor Appl Genet 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Zhang L, Xu J, Ding Y, Cao N, Gao X, Feng Z, Li K, Cheng B, Zhou L, Ren M, Tao Y, Zou G. GWAS of grain color and tannin content in Chinese sorghum based on whole-genome sequencing. Theor Appl Genet 2023; 136:77. [PMID: 36952041 PMCID: PMC10036430 DOI: 10.1007/s00122-023-04307-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Seventy-three QTL related to grain color and tannin content were identified in Chinese sorghum accessions, and a new recessive allelic variant of TAN2 gene was discovered. Sorghum is mainly used for brewing distilled liquors in China. Since grain tannins play an important role in liquor brewing, accurately understanding the relationship between grain color and tannin content can provide basis for selection standards of tannin sorghum. We resequenced a panel of 242 Chinese sorghum accessions and performed population structure and genome-wide association study (GWAS) to identify quantitative trait locus (QTL) affecting pericarp color, testa pigment, and tannin content. Phylogenetic analysis, principal component analysis (PCA), and admixture model were used to infer population structure. Two distinct genetic sub-populations were identified according to their corresponding northern and southern geographic origin. To investigate the genetic basis of natural variation in sorghum grain color, GWAS with 2,760,264 SNPs was conducted in four environments using multiple models (Blink, FarmCPU, GLM, and MLM). Seventy-three QTL were identified to be associated for the color of exocarp, mesocarp, testa, and tannin content on all chromosomes except chromosome 5, of which 47 might be novel QTL. Some important QTL were found to colocalize with orthologous genes in the flavonoid biosynthetic pathway from other plants, including orthologous of Arabidopsis (Arabidopsis thaliana) TT2, TT7, TT12, TT16 and AT5G41220 (GST), as well as orthologous of rice (Oryza sativa) MYB61 and OsbHLH025. Our investigation of the variation in grain color and tannin content in Chinese sorghum germplasm may help guide future sorghum breeding for liquor brewing.
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Affiliation(s)
- Liyi Zhang
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China.
| | - Jianxia Xu
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Yanqing Ding
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Ning Cao
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Xu Gao
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Zhou Feng
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Kuiying Li
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Bing Cheng
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Lengbo Zhou
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Mingjian Ren
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Yuezhi Tao
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Zhejiang Key Laboratory of Digital Dry Land Crops, Hangzhou, 310021, China
| | - Guihua Zou
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Zhejiang Key Laboratory of Digital Dry Land Crops, Hangzhou, 310021, China.
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Zhi X, Hammer G, Borrell A, Tao Y, Wu A, Hunt C, van Oosterom E, Massey-Reed SR, Cruickshank A, Potgieter AB, Jordan D, Mace E, George-Jaeggli B. Genetic basis of sorghum leaf width and its potential as a surrogate for transpiration efficiency. Theor Appl Genet 2022; 135:3057-3071. [PMID: 35933636 PMCID: PMC9482571 DOI: 10.1007/s00122-022-04167-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/27/2022] [Indexed: 06/08/2023]
Abstract
Leaf width was correlated with plant-level transpiration efficiency and associated with 19 QTL in sorghum, suggesting it could be a surrogate for transpiration efficiency in large breeding program. Enhancing plant transpiration efficiency (TE) by reducing transpiration without compromising photosynthesis and yield is a desirable selection target in crop improvement programs. While narrow individual leaf width has been correlated with greater intrinsic water use efficiency in C4 species, the extent to which this translates to greater plant TE has not been investigated. The aims of this study were to evaluate the correlation of leaf width with TE at the whole-plant scale and investigate the genetic control of leaf width in sorghum. Two lysimetry experiments using 16 genotypes varying for stomatal conductance and three field trials using a large sorghum diversity panel (n = 701 lines) were conducted. Negative associations of leaf width with plant TE were found in the lysimetry experiments, suggesting narrow leaves may result in reduced plant transpiration without trade-offs in biomass accumulation. A wide range in width of the largest leaf was found in the sorghum diversity panel with consistent ranking among sorghum races, suggesting that environmental adaptation may have a role in modifying leaf width. Nineteen QTL were identified by genome-wide association studies on leaf width adjusted for flowering time. The QTL identified showed high levels of correspondence with those in maize and rice, suggesting similarities in the genetic control of leaf width across cereals. Three a priori candidate genes for leaf width, previously found to regulate dorsoventrality, were identified based on a 1-cM threshold. This study provides useful physiological and genetic insights for potential manipulation of leaf width to improve plant adaptation to diverse environments.
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Affiliation(s)
- Xiaoyu Zhi
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Henan, China.
| | - Graeme Hammer
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, St Lucia, QLD, Australia
| | - Andrew Borrell
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia
| | - Alex Wu
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, St Lucia, QLD, Australia
| | - Colleen Hunt
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia
- Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Agri-Science Queensland, Warwick, QLD, Australia
| | - Erik van Oosterom
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, St Lucia, QLD, Australia
| | - Sean Reynolds Massey-Reed
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia
| | - Alan Cruickshank
- Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Agri-Science Queensland, Warwick, QLD, Australia
| | - Andries B Potgieter
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Gatton, QLD, Australia
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia.
- Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Agri-Science Queensland, Warwick, QLD, Australia.
| | - Emma Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia.
- Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Agri-Science Queensland, Warwick, QLD, Australia.
| | - Barbara George-Jaeggli
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Centre for Crop Science, The University of Queensland, Warwick, QLD, Australia.
- Department of Agriculture and Fisheries (DAF), Hermitage Research Facility, Agri-Science Queensland, Warwick, QLD, Australia.
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Zhang L, Ding Y, Xu J, Gao X, Cao N, Li K, Feng Z, Cheng B, Zhou L, Ren M, Lu X, Bao Z, Tao Y, Xin Z, Zou G. Selection Signatures in Chinese Sorghum Reveals Its Unique Liquor-Making Properties. Front Plant Sci 2022; 13:923734. [PMID: 35755652 PMCID: PMC9218943 DOI: 10.3389/fpls.2022.923734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Chinese sorghum (S. bicolor) has been a historically critical ingredient for brewing famous distilled liquors ever since Yuan Dynasty (749 ∼ 652 years BP). Incomplete understanding of the population genetics and domestication history limits its broad applications, especially that the lack of genetics knowledge underlying liquor-brewing properties makes it difficult to establish scientific standards for sorghum breeding. To unravel the domestic history of Chinese sorghum, we re-sequenced 244 Chinese sorghum lines selected from 16 provinces. We found that Chinese sorghums formed three distinct genetic sub-structures, referred as the Northern, the Southern, and the Chishui groups, following an obviously geographic pattern. These sorghum accessions were further characterized in liquor brewing traits and identified selection footprints associated with liquor brewing efficiency. An importantly selective sweep region identified includes several homologous genes involving in grain size, pericarp thickness, and architecture of inflorescence. Our result also demonstrated that pericarp strength rather than grain size determines the ability of the grains to resist repeated cooking during brewing process. New insight into the traits beneficial to the liquor-brewing process provides both a better understanding on Chinese sorghum domestication and a guidance on breeding sorghum as a multiple use crop in China.
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Affiliation(s)
- Liyi Zhang
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yanqing Ding
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Jianxia Xu
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Xu Gao
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Ning Cao
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Kuiying Li
- College of Agriculture, Guizhou University, Guiyang, China
| | - Zhou Feng
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
- College of Agriculture, Guizhou University, Guiyang, China
| | - Bing Cheng
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Lengbo Zhou
- Guizhou Institute of Upland Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Mingjian Ren
- College of Agriculture, Guizhou University, Guiyang, China
| | - Xiaochun Lu
- Institute of Sorghum Research, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Zhigui Bao
- Shanghai OE Biotech Co., Ltd., Shanghai, China
| | - Yuezhi Tao
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, United States
| | - Guihua Zou
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Chiluwal A, Perumal R, Poudel HP, Muleta K, Ostmeyer T, Fedenia L, Pokharel M, Bean SR, Sebela D, Bheemanahalli R, Oumarou H, Klein P, Rooney WL, Jagadish SVK. Genetic control of source-sink relationships in grain sorghum. Planta 2022; 255:40. [PMID: 35038036 DOI: 10.1007/s00425-022-03822-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
QTL hotspots identified for selected source-sink-related traits provide the opportunity for pyramiding favorable alleles for improving sorghum productivity under diverse environments. A sorghum bi-parental mapping population was evaluated under six different environments at Hays and Manhattan, Kansas, USA, in 2016 and 2017, to identify genomic regions controlling source-sink relationships. The population consisted of 210 recombinant inbred lines developed from US elite post-flowering drought susceptible (RTx430) and a known post-flowering drought tolerant cultivar (SC35). Selected physiological traits related to source (effective quantum yield of photosystem II and chlorophyll index), sink (grain yield per panicle) and panicle neck diameter were recorded during grain filling. The results showed strong phenotypic and genotypic association between panicle neck diameter and grain yield per panicle during mid-grain filling and at maturity. Multiple QTL model revealed 5-12 including 2-5 major QTL for each trait. Among them 3, 7 and 8 QTL for quantum yield, panicle neck diameter and chlorophyll index, respectively, have not been identified previously in sorghum. Phenotypic variation explained by QTL identified across target traits ranged between 5.5 and 25.4%. Panicle neck diameter and grain yield per panicle were positively associated, indicating the possibility of targeting common co-localized QTL to improve both traits simultaneously through marker-assisted selection. Three major QTL hotspots, controlling multiple traits were identified on chromosome 1 (52.23-61.18 Mb), 2 (2.52-11.43 Mb) and 3 (1.32-3.95 Mb). The identified genomic regions and underlying candidate genes can be utilized in pyramiding favorable alleles for improving source-sink relationships in sorghum under diverse environments.
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Affiliation(s)
- Anuj Chiluwal
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Ramasamy Perumal
- Agricultural Research Center, Kansas State University, Hays, KS, 67601, USA
| | - Hari P Poudel
- Agriculture and Agri-Food Canada, 5403 First Ave. South, Lethbridge, AB, T1J 4B1, Canada
| | - Kebede Muleta
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Troy Ostmeyer
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Lauren Fedenia
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Meghnath Pokharel
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Scott R Bean
- Grain Quality and Structure Research Unit, CGAHR, USDA-ARS, 1515 College Avenue, Manhattan, KS, 66502, USA
| | - David Sebela
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Raju Bheemanahalli
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Halilou Oumarou
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Patricia Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - William L Rooney
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - S V Krishna Jagadish
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA.
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