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Zhang X, Su J, Jia F, He Y, Liao Y, Wang Z, Jiang J, Guan Z, Fang W, Chen F, Zhang F. Genetic architecture and genomic prediction of plant height-related traits in chrysanthemum. HORTICULTURE RESEARCH 2024; 11:uhad236. [PMID: 38222820 PMCID: PMC10782495 DOI: 10.1093/hr/uhad236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/06/2023] [Indexed: 01/16/2024]
Abstract
Plant height (PH) is a crucial trait determining plant architecture in chrysanthemum. To better understand the genetic basis of PH, we investigated the variations of PH, internode number (IN), internode length (IL), and stem diameter (SD) in a panel of 200 cut chrysanthemum accessions. Based on 330 710 high-quality SNPs generated by genotyping by sequencing, a total of 42 associations were identified via a genome-wide association study (GWAS), and 16 genomic regions covering 2.57 Mb of the whole genome were detected through selective sweep analysis. In addition, two SNPs, Chr1_339370594 and Chr18_230810045, respectively associated with PH and SD, overlapped with the selective sweep regions from FST and π ratios. Moreover, candidate genes involved in hormones, growth, transcriptional regulation, and metabolic processes were highlighted based on the annotation of homologous genes in Arabidopsis and transcriptomes in chrysanthemum. Finally, genomic selection for four PH-related traits was performed using a ridge regression best linear unbiased predictor model (rrBLUP) and six marker sets. The marker set constituting the top 1000 most significant SNPs identified via GWAS showed higher predictabilities for the four PH-related traits, ranging from 0.94 to 0.97. These findings improve our knowledge of the genetic basis of PH and provide valuable markers that could be applied in chrysanthemum genomic selection breeding programs.
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Affiliation(s)
- Xuefeng Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210014, China
| | - Jiangshuo Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210014, China
| | - Feifei Jia
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuhua He
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210014, China
| | - Yuan Liao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210014, China
| | - Zhenxing Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210014, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210014, China
| | - Zhiyong Guan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210014, China
| | - Weimin Fang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210014, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210014, China
| | - Fei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Zhongshan Biological Breeding Laboratory, No. 50 Zhongling Street, Nanjing 210014, China
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Kumar N, Boatwright JL, Sapkota S, Brenton ZW, Ballén-Taborda C, Myers MT, Cox WA, Jordan KE, Kresovich S, Boyles RE. Discovering useful genetic variation in the seed parent gene pool for sorghum improvement. Front Genet 2023; 14:1221148. [PMID: 37790706 PMCID: PMC10544336 DOI: 10.3389/fgene.2023.1221148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/04/2023] [Indexed: 10/05/2023] Open
Abstract
Multi-parent populations contain valuable genetic material for dissecting complex, quantitative traits and provide a unique opportunity to capture multi-allelic variation compared to the biparental populations. A multi-parent advanced generation inter-cross (MAGIC) B-line (MBL) population composed of 708 F6 recombinant inbred lines (RILs), was recently developed from four diverse founders. These selected founders strategically represented the four most prevalent botanical races (kafir, guinea, durra, and caudatum) to capture a significant source of genetic variation to study the quantitative traits in grain sorghum [Sorghum bicolor (L.) Moench]. MBL was phenotyped at two field locations for seven yield-influencing traits: panicle type (PT), days to anthesis (DTA), plant height (PH), grain yield (GY), 1000-grain weight (TGW), tiller number per meter (TN) and yield per panicle (YPP). High phenotypic variation was observed for all the quantitative traits, with broad-sense heritabilities ranging from 0.34 (TN) to 0.84 (PH). The entire population was genotyped using Diversity Arrays Technology (DArTseq), and 8,800 single nucleotide polymorphisms (SNPs) were generated. A set of polymorphic, quality-filtered markers (3,751 SNPs) and phenotypic data were used for genome-wide association studies (GWAS). We identified 52 marker-trait associations (MTAs) for the seven traits using BLUPs generated from replicated plots in two locations. We also identified desirable allelic combinations based on the plant height loci (Dw1, Dw2, and Dw3), which influences yield related traits. Additionally, two novel MTAs were identified each on Chr1 and Chr7 for yield traits independent of dwarfing genes. We further performed a multi-variate adaptive shrinkage analysis and 15 MTAs with pleiotropic effect were identified. The five best performing MBL progenies were selected carrying desirable allelic combinations. Since the MBL population was designed to capture significant diversity for maintainer line (B-line) accessions, these progenies can serve as valuable resources to develop superior sorghum hybrids after validation of their general combining abilities via crossing with elite pollinators. Further, newly identified desirable allelic combinations can be used to enrich the maintainer germplasm lines through marker-assisted backcross breeding.
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Affiliation(s)
- Neeraj Kumar
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - J. Lucas Boatwright
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Sirjan Sapkota
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
| | - Zachary W. Brenton
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Carolina Seed Systems, Darlington, SC, United States
| | - Carolina Ballén-Taborda
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Pee Dee Research and Education Center, Clemson University, Florence, SC, United States
| | - Matthew T. Myers
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - William A. Cox
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Kathleen E. Jordan
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Stephen Kresovich
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Feed the Future Innovation Lab for Crop Improvement, Cornell University, Ithaca, NY, United States
| | - Richard E. Boyles
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Pee Dee Research and Education Center, Clemson University, Florence, SC, United States
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Haile M, Ro N, Ko HC, Oh H, Lee GA. A Comprehensive Genome-Wide Association Study of Carotenoid and Capsaicinoid Contents in Capsicum chinense Germplasm. Int J Mol Sci 2023; 24:13885. [PMID: 37762188 PMCID: PMC10531199 DOI: 10.3390/ijms241813885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Pepper is a highly important vegetable globally, both economically and nutritionally. However, to efficiently select and identify genetic resources for pepper breeding programs, it is crucial to understand the association between important traits and genetic factors. In this study, we investigated the genetic basis of carotenoid and capsaicinoid content in 160 Capsicum chinense germplasms. The study observed significant variability in carotenoid and capsaicinoid content among the germplasms. Correlation analysis revealed a strong positive correlation between violaxanthin and antheraxanthin. In contrast, capsaicin and dihydrocapsaicin displayed negative correlations with individual carotenoids but exhibited a strong positive correlation between the two compounds (r = 0.90 ***). Genotyping-by-sequencing (GBS) was performed on 160 genotypes of pepper germplasm, which identified 47,810 high-quality SNPs. A comprehensive genome-wide association analysis was performed using these SNPs to identify SNPs associated with carotenoids and capsaicinoids, revealing 193 SNPs that exhibited significant associations. Specifically, 4 SNPs were associated with violaxanthin, 2 with antheraxanthin, 86 with capsorubin, 5 with capsanthin, 63 with zeaxanthin, 3 with β-cryptoxanthin, and 2 with α-carotene. With further studies, the significantly associated SNPs identified in this study have the potential to be utilized for selecting pepper accessions with high carotenoid and capsaicinoid contents. Additionally, the genes associated with these significant SNPs will be used to understand their roles and involvement in the biosynthesis pathway of carotenoids and capsaicinoids. Understanding the function of these genes can provide insights into the molecular mechanisms underlying the production of these bioactive compounds in pepper. The findings of this study hold valuable implications for selecting pepper varieties with desirable traits and developing breeding programs aimed at enhancing the nutritional and medicinal properties of pepper.
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Guden B, Yol E, Erdurmus C, Lucas SJ, Uzun B. Construction of a high-density genetic linkage map and QTL mapping for bioenergy-related traits in sweet sorghum [ Sorghum bicolor (L.) Moench]. FRONTIERS IN PLANT SCIENCE 2023; 14:1081931. [PMID: 37342135 PMCID: PMC10278949 DOI: 10.3389/fpls.2023.1081931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/15/2023] [Indexed: 06/22/2023]
Abstract
Sorghum is an important but arguably undervalued cereal crop, grown in large areas in Asia and Africa due to its natural resilience to drought and heat. There is growing demand for sweet sorghum as a source of bioethanol as well as food and feed. The improvement of bioenergy-related traits directly affects bioethanol production from sweet sorghum; therefore, understanding the genetic basis of these traits would enable new cultivars to be developed for bioenergy production. In order to reveal the genetic architecture behind bioenergy-related traits, we generated an F2 population from a cross between sweet sorghum cv. 'Erdurmus' and grain sorghum cv. 'Ogretmenoglu'. This was used to construct a genetic map from SNPs discovered by double-digest restriction-site associated DNA sequencing (ddRAD-seq). F3 lines derived from each F2 individual were phenotyped for bioenergy-related traits in two different locations and their genotypes were analyzed with the SNPs to identify QTL regions. On chromosomes 1, 7, and 9, three major plant height (PH) QTLs (qPH1.1, qPH7.1, and qPH9.1) were identified, with phenotypic variation explained (PVE) ranging from 10.8 to 34.8%. One major QTL (qPJ6.1) on chromosome 6 was associated with the plant juice trait (PJ) and explained 35.2% of its phenotypic variation. For fresh biomass weight (FBW), four major QTLs (qFBW1.1, qFBW6.1, qFBW7.1, and qFBW9.1) were determined on chromosomes 1, 6, 7, and 9, which explained 12.3, 14.5, 10.6, and 11.9% of the phenotypic variation, respectively. Moreover, two minor QTLs (qBX3.1 and qBX7.1) of Brix (BX) were mapped on chromosomes 3 and 7, explaining 8.6 and 9.7% of the phenotypic variation, respectively. The QTLs in two clusters (qPH7.1/qBX7.1 and qPH7.1/qFBW7.1) overlapped for PH, FBW and BX. The QTL, qFBW6.1, has not been previously reported. In addition, eight SNPs were converted into cleaved amplified polymorphic sequences (CAPS) markers, which can be easily detected by agarose gel electrophoresis. These QTLs and molecular markers can be used for pyramiding and marker-assisted selection studies in sorghum, to develop advanced lines that include desirable bioenergy-related traits.
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Affiliation(s)
- Birgul Guden
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Engin Yol
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Cengiz Erdurmus
- Department of Field Crops, West Mediterranean Agricultural Research Institute, Antalya, Türkiye
| | - Stuart James Lucas
- Sabanci University Nanotechnology Research and Application Centre, Sabanci University, Istanbul, Türkiye
| | - Bulent Uzun
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
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Zhang Y, Fan X, Liang D, Guo Q, Zhang X, Nie M, Li C, Meng S, Zhang X, Xu P, Guo W, Wang H, Liu Q, Wu Y. The Identification of a Yield-Related Gene Controlling Multiple Traits Using GWAS in Sorghum ( Sorghum bicolor L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1557. [PMID: 37050183 PMCID: PMC10097259 DOI: 10.3390/plants12071557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Sorghum bicolor (L.) is one of the oldest crops cultivated by human beings which has been used in food and wine making. To understand the genetic diversity of sorghum breeding resources and further guide molecular-marker-assisted breeding, six yield-related traits were analyzed for 214 sorghum germplasm from all over the world, and 2,811,016 single-nucleotide polymorphisms (SNPs) markers were produced by resequencing these germplasms. After controlling Q and K, QTLs were found to be related to the traits using three algorisms. Interestingly, an important QTL was found which may affect multiple traits in this study. It was the most likely candidate gene for the gene SORBI_3008G116500, which was a homolog of Arabidopsis thaliana gene-VIP5 found by analyzing the annotation of the gene in the LD block. The haplotype analysis showed that the SORBI_3008G116500hap3 was the elite haplotype, and it only existed in Chinese germplasms. The traits were proven to be more associated with the SNPs of the SORBI_3008G116500 promoter through gene association studies. Overall, the QTLs and the genes identified in this study would benefit molecular-assisted yield breeding in sorghum.
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Affiliation(s)
- Yizhong Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Xinqi Fan
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Du Liang
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Qi Guo
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Xiaojuan Zhang
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Mengen Nie
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Chunhong Li
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Shan Meng
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xianggui Zhang
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Peng Xu
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Wenqi Guo
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Huiyan Wang
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
- Sorghum Research Institute, Shanxi Key Laboratory of Sorghum Genetic and Germplasm Innovation, Shanxi Agricultural University, Yuci 030600, China
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Qingshan Liu
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, State Key Laboratory of Sustainable Dryland Agriculture (In Preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Yuxiang Wu
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
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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. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:77. [PMID: 36952041 PMCID: PMC10036430 DOI: 10.1007/s00122-023-04307-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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Adedugba AA, Adeyemo OA, Adetumbi AJ, Amusa OD, Ogunkanmi LA. Evaluation of genetic variability for major agro-morphological and stalk sugar traits in African sorghum genotypes. Heliyon 2023; 9:e14622. [PMID: 36994400 PMCID: PMC10040710 DOI: 10.1016/j.heliyon.2023.e14622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 03/22/2023] Open
Abstract
The study aimed to assess one hundred and twelve (112) accessions of sorghum sourced from Nigeria and other four African countries for their genetic variability, heritability (broad sense) and genetic advance components to identify promising accessions with high grain yield and sweet stalk which can serve as future parents for breeding dual-purpose lines. The accessions were evaluated at Ilora, Oyo State, Nigeria in a randomized complete block design (RCBD) layout with three replicates in two planting seasons (2020 and 2021). The results showed that the phenotypic coefficient of variation (PCV) was higher than the genotypic coefficient of variation (GCV). The highest PCV and GCV were grain yield (51.89%) and inflorescence length (42.26%), respectively, while a hundred seed grain weight had the lowest PCV (17.83%) and GCV (21.55%). The range of genetic advance over mean (GAM) was 28.33% for leaf width and 81.62% for inflorescence length. Inflorescence length had the highest values of heritability and GAM (0.88, 81.62%), while a low value was obtained for grain yield (0.27, 29.32%). Twenty-two accessions had higher grain yields than the yields of check varieties. The high-yielding accessions, SG57, SG31, SG06, and SG12 had grain yields of 3.07 t/ha, 2.89 t/ha, 2.76 t/ha and 2.73 t/ha, respectively. Fourteen accessions had wet stalks, of which 12 of the accessions had soluble stalk sugar (Brix) above 12%, which is comparable to the amount found in sweet sorghum. Three accessions with Brix above 12% (SG16, SG31, SG32) and high grain yields (2.32 t/ha, 2.89 t/ha and 2.02 t/ha) were identified as promising accessions. There is considerable genetic diversity among African sorghum accessions in Nigeria's southwest agroecosystem, which should improve food security and breeding potential.
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Kumar P, Singh J, Kaur G, Adunola PM, Biswas A, Bazzer S, Kaur H, Kaur I, Kaur H, Sandhu KS, Vemula S, Kaur B, Singh V, Tseng TM. OMICS in Fodder Crops: Applications, Challenges, and Prospects. Curr Issues Mol Biol 2022; 44:5440-5473. [PMID: 36354681 PMCID: PMC9688858 DOI: 10.3390/cimb44110369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 09/08/2024] Open
Abstract
Biomass yield and quality are the primary targets in forage crop improvement programs worldwide. Low-quality fodder reduces the quality of dairy products and affects cattle's health. In multipurpose crops, such as maize, sorghum, cowpea, alfalfa, and oat, a plethora of morphological and biochemical/nutritional quality studies have been conducted. However, the overall growth in fodder quality improvement is not on par with cereals or major food crops. The use of advanced technologies, such as multi-omics, has increased crop improvement programs manyfold. Traits such as stay-green, the number of tillers per plant, total biomass, and tolerance to biotic and/or abiotic stresses can be targeted in fodder crop improvement programs. Omic technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, provide an efficient way to develop better cultivars. There is an abundance of scope for fodder quality improvement by improving the forage nutrition quality, edible quality, and digestibility. The present review includes a brief description of the established omics technologies for five major fodder crops, i.e., sorghum, cowpea, maize, oats, and alfalfa. Additionally, current improvements and future perspectives have been highlighted.
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Affiliation(s)
- Pawan Kumar
- Agrotechnology Division, Council of Scientific and Industrial Research-Institute of Himalayan Bioresource Technology, Palampur 176061, India
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India
| | - Jagmohan Singh
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India
- Krishi Vigyan Kendra, Guru Angad Dev Veterinary and Animal Science University, Barnala 148107, India
| | - Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | | | - Anju Biswas
- Agronomy Department, University of Florida, Gainesville, FL 32611, USA
| | - Sumandeep Bazzer
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, WA 57007, USA
| | - Harpreet Kaur
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88001, USA
| | - Ishveen Kaur
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Harpreet Kaur
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Karansher Singh Sandhu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99163, USA
| | - Shailaja Vemula
- Agronomy Department, UF/IFAS Research and Education Center, Belle Glade, FL 33430, USA
| | - Balwinder Kaur
- Department of Entomology, UF/IFAS Research and Education Center, Belle Glade, FL 33430, USA
| | - Varsha Singh
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS 39759, USA
| | - Te Ming Tseng
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS 39759, USA
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9
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Enyew M, Feyissa T, Carlsson AS, Tesfaye K, Hammenhag C, Seyoum A, Geleta M. Genome-wide analyses using multi-locus models revealed marker-trait associations for major agronomic traits in Sorghum bicolor. FRONTIERS IN PLANT SCIENCE 2022; 13:999692. [PMID: 36275578 PMCID: PMC9585286 DOI: 10.3389/fpls.2022.999692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/14/2022] [Indexed: 06/01/2023]
Abstract
Globally, sorghum is the fifth most important cereal crop, and it is a major crop in Ethiopia, where it has a high genetic diversity. The country's sorghum gene pool contributes significantly to sorghum improvement worldwide. This study aimed to identify genomic regions and candidate genes associated with major agronomic traits in sorghum by using its genetic resources in Ethiopia for a genome-wide association study (GWAS). Phenotypic data of days to flowering (DTF), plant height (PH), panicle length (PALH), panicle width (PAWD), panicle weight (PAWT), and grain yield (GY) were collected from a GWAS panel comprising 324 sorghum accessions grown in three environments. SeqSNP, a targeted genotyping method, was used to genotype the panel using 5,000 gene-based single nucleotide polymorphism (SNP) markers. For marker-trait association (MTA) analyses, fixed and random model circulating probability unification (FarmCPU), and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) models were used. In all traits, high phenotypic variation was observed, with broad-sense heritability ranging from 0.32 (for GY) to 0.90 (for PALH). A population structure, principal component analysis, and kinship analysis revealed that the accessions could be divided into two groups. In total, 54 MTAs were identified, 11 of which were detected by both BLINK and farmCPU. MTAs identified for each trait ranged from five (PAWT and GY) to fourteen (PH) representing both novel and previously identified quantitative trait loci (QTLs). Three SNPs were associated with more than one trait, including a SNP within the Sobic.004G189200 gene that was associated with PH and PAWT. Major effect SNP loci, Sbi2393610 (PVE = 23.3%), Sbi10438246 (PVE = 35.2%), Sbi17789352 (PVE = 11.9%) and Sbi30169733 (PVE = 18.9%) on chromosomes 1, 3, 5 and 9 that showed strong association signals for PAWD, DTF, GY and PALH, respectively, were major findings of this study. The SNP markers and candidate genes identified in this study provide insights into the genetic control of grain yield and related agronomic traits, and once validated, the markers could be used in genomics-led breeding.
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Affiliation(s)
- Muluken Enyew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Tileye Feyissa
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Anders S. Carlsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Amare Seyoum
- National Sorghum Research Program, Crop Research Department, Melkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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10
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Dong H, Birhan T, Abajebel N, Wakjira M, Mitiku T, Lemke C, Vadez V, Paterson AH, Bantte K. Natural variation further increases resilience of sorghum bred for chronically drought-prone environments. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5730-5744. [PMID: 35605043 DOI: 10.1093/jxb/erac217] [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: 12/13/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Drought stress is one of the major constraints for crop production in the Sahel region of Africa. Here, we explore the potential to use natural genetic variation to build on the inherent drought tolerance of an elite sorghum cultivar, Teshale, that has been bred for Ethiopian conditions including chronic drought. We evaluated a backcross nested-association mapping population using 12 diverse founder lines crossed with Teshale under three drought-prone environments in Ethiopia. All 12 populations averaged higher head exsertion and lower leaf senescence than the recurrent parent in the two most stressful environments, reflecting new drought resilience mechanisms from the donors. A total of 154 quantitative trait loci (QTLs) were detected for eight drought-responsive traits, and their validity was supported by the fact that 113 (73.4%) overlapped with QTLs previously detected for the same traits, concentrated in regions previously associated with 'stay-green' traits. Allele effects showed that some favourable alleles are already present in the Ethiopian cultivar; however, the exotic donors offer rich scope for increasing drought resilience. Using model-selected SNPs associated with the eight traits identified in this study and three in a companion study, phenotypic prediction accuracies for grain yield were equivalent to genome-wide SNPs and were significantly better than random SNPs, indicating that the selected traits are predictive of sorghum grain yield.
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Affiliation(s)
- Hongxu Dong
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, USA
| | - Techale Birhan
- Department of Horticulture and Plant Science, Jimma University, Ethiopia
| | - Nezif Abajebel
- Department of Horticulture and Plant Science, Jimma University, Ethiopia
| | - Misganu Wakjira
- Department of Horticulture and Plant Science, Jimma University, Ethiopia
| | - Tesfaye Mitiku
- Department of Horticulture and Plant Science, Jimma University, Ethiopia
| | - Cornelia Lemke
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, USA
| | | | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, USA
| | - Kassahun Bantte
- Department of Horticulture and Plant Science, Jimma University, Ethiopia
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11
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Petersen KB, Kellogg EA. Diverse ecological functions and the convergent evolution of grass awns. AMERICAN JOURNAL OF BOTANY 2022; 109:1331-1345. [PMID: 36048829 PMCID: PMC9828495 DOI: 10.1002/ajb2.16060] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
The awn of grasses is a long, conspicuous outgrowth of the floral bracts in a grass spikelet. It is known to impact agricultural yield, but we know little about its broader ecological function, nor the selective forces that lead to its evolution. Grass awns are phenotypically diverse across the extant ~12,000 species of Poaceae. Awns have been lost and gained repeatedly over evolutionary time, between and within lineages, suggesting that they could be under selection and might provide adaptive benefit in some environments. Despite the phylogenetic context, we know of no studies that have tested whether the origin of awns correlates with putative selective forces on their form and function. Presence or absence of awns is not plastic; rather, heritability is high. The awns of grasses often are suggested as adaptations for dispersal, and most experimental work has been aimed at testing this hypothesis. Proposed dispersal functions include soil burial, epizoochory, and aerial orientation. Awns may also protect the seed from drought, herbivores, or fire by helping it become buried in soil. We do not fully understand the fitness or nutrient costs of awn production, but in some species awns function in photosynthesis, providing carbon to the seed. Here we show that awns likely provide an adaptive advantage, but argue that studies on awn function have lacked critical phylogenetic information to demonstrate adaptive convergent evolution, are taxonomically biased, and often lack clear alternative hypotheses.
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12
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Takanashi H, Kajiya-Kanegae H, Nishimura A, Yamada J, Ishimori M, Kobayashi M, Yano K, Iwata H, Tsutsumi N, Sakamoto W. DOMINANT AWN INHIBITOR Encodes the ALOG Protein Originating from Gene Duplication and Inhibits AWN Elongation by Suppressing Cell Proliferation and Elongation in Sorghum. PLANT & CELL PHYSIOLOGY 2022; 63:901-918. [PMID: 35640621 DOI: 10.1093/pcp/pcac057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 04/21/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
The awn, a needle-like structure extending from the tip of the lemma in grass species, plays a role in environmental adaptation and fitness. In some crops, awns appear to have been eliminated during domestication. Although numerous genes involved in awn development have been identified, several dominant genes that eliminate awns are also known to exist. For example, in sorghum (Sorghum bicolor), the dominant awn-inhibiting gene has been known since 1921; however, its molecular features remain uncharacterized. In this study, we conducted quantitative trait locus analysis and a genome-wide association study of awn-related traits in sorghum and identified DOMINANT AWN INHIBITOR (DAI), which encodes the ALOG family protein on chromosome 3. DAI appeared to be present in most awnless sorghum cultivars, likely because of its effectiveness. Detailed analysis of the ALOG protein family in cereals revealed that DAI originated from a duplication of its twin paralog (DAIori) on chromosome 10. Observations of immature awns in near-isogenic lines revealed that DAI inhibits awn elongation by suppressing both cell proliferation and elongation. We also found that only DAI gained a novel function to inhibit awn elongation through an awn-specific expression pattern distinct from that of DAIori. Interestingly, heterologous expression of DAI with its own promoter in rice inhibited awn elongation in the awned cultivar Kasalath. We found that DAI originated from gene duplication, providing an interesting example of gain-of-function that occurs only in sorghum but shares its functionality with rice and sorghum.
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Affiliation(s)
- Hideki Takanashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Hiromi Kajiya-Kanegae
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Kouwa Nishi-Shimbashi Bldg. 5f, 2-14-1 Nishi-Shimbashi, Minato-ku, Tokyo 105-0003, Japan
| | - Asuka Nishimura
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Junko Yamada
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Motoyuki Ishimori
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Masaaki Kobayashi
- Department of Life Sciences, Faculty of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Kentaro Yano
- Department of Life Sciences, Faculty of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, 214-8571 Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Nobuhiro Tsutsumi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046 Japan
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13
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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] [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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14
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Kong W, Nabukalu P, Cox TS, Goff V, Robertson JS, Pierce G, Lemke C, Compton R, Reeves J, Paterson AH. Comparative evolution of vegetative branching in sorghum. PLoS One 2021; 16:e0255922. [PMID: 34388196 PMCID: PMC8362987 DOI: 10.1371/journal.pone.0255922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/26/2021] [Indexed: 11/19/2022] Open
Abstract
Tillering and secondary branching are two plastic traits with high agronomic importance, especially in terms of the ability of plants to adapt to changing environments. We describe a quantitative trait analysis of tillering and secondary branching in two novel BC1F2 populations totaling 246 genotypes derived from backcrossing two Sorghum bicolor x S. halepense F1 plants to a tetraploidized S. bicolor. A two-year, two-environment phenotypic evaluation in Bogart, GA and Salina, KS permitted us to identify major effect and environment specific QTLs. Significant correlation between tillering and secondary branching followed by discovery of overlapping sets of QTLs continue to support the developmental relationship between these two organs and suggest the possibility of pleiotropy. Comparisons with two other populations sharing S. bicolor BTx623 as a common parent but sampling the breadth of the Sorghum genus, increase confidence in QTL detected for these two plastic traits and provide insight into the evolution of morphological diversity in the Eusorghum clade. Correspondence between flowering time and vegetative branching supports other evidence in suggesting a pleiotropic effect of flowering genes. We propose a model to predict biomass weight from plant architecture related traits, quantifying contribution of each trait to biomass and providing guidance for future breeding experiments.
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Affiliation(s)
- WenQian Kong
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States of America
- Department of Statistics, University of Georgia, Athens, Georgia, United States of America
| | | | - T. Stan Cox
- The Land Institute, Salina, Kansas, United States of America
| | - Valorie Goff
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States of America
| | - Jon S. Robertson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States of America
| | - Gary Pierce
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States of America
| | - Cornelia Lemke
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States of America
| | - Rosana Compton
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States of America
| | - Jaxk Reeves
- Department of Statistics, University of Georgia, Athens, Georgia, United States of America
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, United States of America
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15
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Boatwright JL, Brenton ZW, Boyles RE, Sapkota S, Myers MT, Jordan KE, Dale SM, Shakoor N, Cooper EA, Morris GP, Kresovich S. Genetic characterization of a Sorghum bicolor multiparent mapping population emphasizing carbon-partitioning dynamics. G3-GENES GENOMES GENETICS 2021; 11:6157831. [PMID: 33681979 PMCID: PMC8759819 DOI: 10.1093/g3journal/jkab060] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/18/2021] [Indexed: 12/03/2022]
Abstract
Sorghum bicolor, a photosynthetically efficient C4 grass, represents an important source of grain, forage, fermentable sugars, and cellulosic fibers that can be utilized in myriad applications ranging from bioenergy to bioindustrial feedstocks. Sorghum’s efficient fixation of carbon per unit time per unit area per unit input has led to its classification as a preferred biomass crop highlighted by its designation as an advanced biofuel by the U.S. Department of Energy. Due to its extensive genetic diversity and worldwide colonization, sorghum has considerable diversity for a range of phenotypes influencing productivity, composition, and sink/source dynamics. To dissect the genetic basis of these key traits, we present a sorghum carbon-partitioning nested association mapping (NAM) population generated by crossing 11 diverse founder lines with Grassl as the single recurrent female. By exploiting existing variation among cellulosic, forage, sweet, and grain sorghum carbon partitioning regimes, the sorghum carbon-partitioning NAM population will allow the identification of important biomass-associated traits, elucidate the genetic architecture underlying carbon partitioning and improve our understanding of the genetic determinants affecting unique phenotypes within Poaceae. We contrast this NAM population with an existing grain population generated using Tx430 as the recurrent female. Genotypic data are assessed for quality by examining variant density, nucleotide diversity, linkage decay, and are validated using pericarp and testa phenotypes to map known genes affecting these phenotypes. We release the 11-family NAM population along with corresponding genomic data for use in genetic, genomic, and agronomic studies with a focus on carbon-partitioning regimes.
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Affiliation(s)
- J Lucas Boatwright
- Advanced Plant Technology, Clemson University, Clemson, SC 29634, USA.,Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA
| | - Zachary W Brenton
- Advanced Plant Technology, Clemson University, Clemson, SC 29634, USA.,Carolina Seed Systems, Darlington, SC 29532, USA
| | - Richard E Boyles
- Advanced Plant Technology, Clemson University, Clemson, SC 29634, USA.,Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA
| | - Sirjan Sapkota
- Advanced Plant Technology, Clemson University, Clemson, SC 29634, USA
| | - Matthew T Myers
- Advanced Plant Technology, Clemson University, Clemson, SC 29634, USA
| | - Kathleen E Jordan
- Advanced Plant Technology, Clemson University, Clemson, SC 29634, USA
| | - Savanah M Dale
- Advanced Plant Technology, Clemson University, Clemson, SC 29634, USA
| | - Nadia Shakoor
- Donald Danforth Plant Science Center, St. Louis, MI 63132, USA
| | - Elizabeth A Cooper
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC 27705, USA
| | - Geoffrey P Morris
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | - Stephen Kresovich
- Advanced Plant Technology, Clemson University, Clemson, SC 29634, USA.,Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA
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16
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Hao H, Li Z, Leng C, Lu C, Luo H, Liu Y, Wu X, Liu Z, Shang L, Jing HC. Sorghum breeding in the genomic era: opportunities and challenges. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1899-1924. [PMID: 33655424 PMCID: PMC7924314 DOI: 10.1007/s00122-021-03789-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/05/2021] [Indexed: 05/04/2023]
Abstract
The importance and potential of the multi-purpose crop sorghum in global food security have not yet been fully exploited, and the integration of the state-of-art genomics and high-throughput technologies into breeding practice is required. Sorghum, a historically vital staple food source and currently the fifth most important major cereal, is emerging as a crop with diverse end-uses as food, feed, fuel and forage and a model for functional genetics and genomics of tropical grasses. Rapid development in high-throughput experimental and data processing technologies has significantly speeded up sorghum genomic researches in the past few years. The genomes of three sorghum lines are available, thousands of genetic stocks accessible and various genetic populations, including NAM, MAGIC, and mutagenised populations released. Functional and comparative genomics have elucidated key genetic loci and genes controlling agronomical and adaptive traits. However, the knowledge gained has far away from being translated into real breeding practices. We argue that the way forward is to take a genome-based approach for tailored designing of sorghum as a multi-functional crop combining excellent agricultural traits for various end uses. In this review, we update the new concepts and innovation systems in crop breeding and summarise recent advances in sorghum genomic researches, especially the genome-wide dissection of variations in genes and alleles for agronomically important traits. Future directions and opportunities for sorghum breeding are highlighted to stimulate discussion amongst sorghum academic and industrial communities.
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Affiliation(s)
- Huaiqing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zhigang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Chuanyuan Leng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Cheng Lu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanming Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhiquan Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Li Shang
- 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.
- Engineering Laboratory for Grass-based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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17
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Mural RV, Grzybowski M, Miao C, Damke A, Sapkota S, Boyles RE, Salas Fernandez MG, Schnable PS, Sigmon B, Kresovich S, Schnable JC. Meta-Analysis Identifies Pleiotropic Loci Controlling Phenotypic Trade-offs in Sorghum. Genetics 2021; 218:6294935. [PMID: 34100945 PMCID: PMC9335936 DOI: 10.1093/genetics/iyab087] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/07/2021] [Indexed: 01/03/2023] Open
Abstract
Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome wide association studies conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35-43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations.
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Affiliation(s)
- Ravi V Mural
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Marcin Grzybowski
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Chenyong Miao
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Alyssa Damke
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Sirjan Sapkota
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634 USA.,Department of Plant and Environment Sciences, Clemson University, Clemson, SC 29634 USA
| | - Richard E Boyles
- Department of Plant and Environment Sciences, Clemson University, Clemson, SC 29634 USA.,Pee Dee Research and Education Center, Clemson University, Florence, SC 29532 USA
| | | | | | - Brandi Sigmon
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
| | - Stephen Kresovich
- Department of Plant and Environment Sciences, Clemson University, Clemson, SC 29634 USA.,Feed the Future Innovation Lab for Crop Improvement Cornell University, Ithaca, NY 14850 USA
| | - James C Schnable
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588 USA
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18
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Genetic dissection of QTLs associated with spikelet-related traits and grain size in sorghum. Sci Rep 2021; 11:9398. [PMID: 33931706 PMCID: PMC8087780 DOI: 10.1038/s41598-021-88917-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
Although spikelet-related traits such as size of anther, spikelet, style, and stigma are associated with sexual reproduction in grasses, no QTLs have been reported in sorghum. Additionally, there are only a few reports on sorghum QTLs related to grain size, such as grain length, width, and thickness. In this study, we performed QTL analyses of nine spikelet-related traits (length of sessile spikelet, pedicellate spikelet, pedicel, anther, style, and stigma; width of sessile spikelet and stigma; and stigma pigmentation) and six grain-related traits (length, width, thickness, length/width ratio, length/thickness ratio, and width/thickness ratio) using sorghum recombinant inbred lines. We identified 36 and 7 QTLs for spikelet-related traits and grain-related traits, respectively, and found that most sorghum spikelet organ length- and width-related traits were partially controlled by the dwarf genes Dw1 and Dw3. Conversely, we found that these Dw genes were not strongly involved in the regulation of grain size. The QTLs identified in this study aid in understanding the genetic basis of spikelet- and grain-related traits in sorghum.
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19
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Wondimu Z, Dong H, Paterson AH, Worku W, Bantte K. Genetic diversity, population structure and selection signature in Ethiopian Sorghum (Sorghum bicolor L. [Moench]) germplasm. G3-GENES GENOMES GENETICS 2021; 11:6237486. [PMID: 33871028 PMCID: PMC8495740 DOI: 10.1093/g3journal/jkab087] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/07/2021] [Indexed: 11/17/2022]
Abstract
Ethiopia, the probable center of origin and diversity for sorghum [Sorghum bicolor L. (Moench)] and with unique ecogeographic features, possesses a large number of sorghum landraces that have not been well studied. Increased knowledge of this diverse germplasm through large-scale genomic characterization may contribute for understanding of evolutionary biology, and adequate use of these valuable resources from the center of origin. In this study, we characterized genetic diversity, population structure and selection signature in 304 sorghum accessions collected from diverse sorghum growing regions of Ethiopia using genotyping-by-sequencing. We identified a total of 108,107 high-quality single-nucleotide polymorphism (SNPs) markers that were evenly distributed across the sorghum genome. The average gene diversity among accessions was high (He = 0.29). We detected a relatively low frequency of rare alleles (26%), highlighting the potential of this germplasm for subsequent allele mining studies through genome-wide association studies. Although we found no evidence of genetic differentiation among administrative regions (FST = 0.02, P = 0.12), population structure and cluster analyses showed clear differentiation among six Ethiopian sorghum populations (FST = 0.28, P = 0.01) adapting to different environments. Analysis of SNP differentiation between the identified genetic groups revealed a total of 40 genomic regions carrying signatures of selection. These regions harbored candidate genes potentially involved in a variety of biological processes, including abiotic stress tolerance, pathogen defense and reproduction. Overall, a high level of untapped diversity for sorghum improvement remains available in Ethiopia, with patterns of diversity consistent with divergent selection on a range of adaptive characteristics.
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Affiliation(s)
- Zeleke Wondimu
- College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
| | - Hongxu Dong
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
| | - Walelign Worku
- College of Agriculture, Hawassa University, PO Box 05, Hawassa, Ethiopia
| | - Kassahun Bantte
- College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
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20
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Kong W, Nabukalu P, Cox TS, Goff VH, Robertson JS, Pierce GJ, Lemke C, Compton R, Paterson AH. Quantitative trait mapping of plant architecture in two BC 1F 2 populations of Sorghum Bicolor × S. halepense and comparisons to two other sorghum populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1185-1200. [PMID: 33423085 DOI: 10.1007/s00122-020-03763-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
Comparing populations derived, respectively, from polyploid Sorghum halepense and its progenitors improved knowledge of plant architecture and showed that S. halepense harbors genetic novelty of potential value for sorghum improvement Vegetative growth and the timing of the vegetative-to-reproductive transition are critical to a plant's fitness, directly and indirectly determining when and how a plant lives, grows and reproduces. We describe quantitative trait analysis of plant height and flowering time in the naturally occurring tetraploid Sorghum halepense, using two novel BC1F2 populations totaling 246 genotypes derived from backcrossing two tetraploid Sorghum bicolor x S. halepense F1 plants to a tetraploidized S. bicolor. Phenotyping for two years each in Bogart, GA and Salina, KS allowed us to dissect variance into narrow-sense genetic (QTLs) and environmental components. In crosses with a common S. bicolor BTx623 parent, comparison of QTLs in S. halepense, its rhizomatous progenitor S. propinquum and S. bicolor race guinea which is highly divergent from BTx623 permit inferences of loci at which new alleles have been associated with improvement of elite sorghums. The relative abundance of QTLs unique to the S. halepense populations may reflect its polyploidy and subsequent 'diploidization' processes often associated with the formation of genetic novelty, a possibility further supported by a high level of QTL polymorphism within sibling lines derived from a common S. halepense parent. An intriguing hypothesis for further investigation is that polyploidy of S. halepense following 96 million years of abstinence, coupled with natural selection during its spread to diverse environments across six continents, may provide a rich collection of novel alleles that offer potential opportunities for sorghum improvement.
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Affiliation(s)
- WenQian Kong
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Rd, Athens, GA, 30602, USA
| | - Pheonah Nabukalu
- The Land Institute, 2440 E Water Well Rd, Salina, KS, 67401, USA
| | - T S Cox
- The Land Institute, 2440 E Water Well Rd, Salina, KS, 67401, USA
| | - Valorie H Goff
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Rd, Athens, GA, 30602, USA
| | - Jon S Robertson
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Rd, Athens, GA, 30602, USA
| | - Gary J Pierce
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Rd, Athens, GA, 30602, USA
| | - Cornelia Lemke
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Rd, Athens, GA, 30602, USA
| | - Rosana Compton
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Rd, Athens, GA, 30602, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Rd, Athens, GA, 30602, USA.
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21
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Menamo T, Kassahun B, Borrell AK, Jordan DR, Tao Y, Hunt C, Mace E. Genetic diversity of Ethiopian sorghum reveals signatures of climatic adaptation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:731-742. [PMID: 33341904 DOI: 10.1007/s00122-020-03727-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/06/2020] [Indexed: 05/23/2023]
Abstract
A large collection of Ethiopian sorghum landraces, characterized by agro-ecology and racial-group, was found to contain high levels of diversity and admixture, with significant SNP associations identified for environmental adaptation. Sorghum [Sorghum bicolor L. (Moench)] is a major staple food crop in Ethiopia, exhibiting extensive genetic diversity with adaptations to diverse agroecologies. The environmental and climatic drivers, as well as the genomic basis of adaptation, are poorly understood in Ethiopian sorghum and are critical elements for the development of climate-resilient crops. Exploration of the genome-environment association (GEA) is important for identifying adaptive loci and predicting phenotypic variation. The current study aimed to better understand the GEA of a large collection of Ethiopian sorghum landraces (n = 940), characterized with genome-wide SNP markers, to investigate key traits related to adaptation to temperature, precipitation and altitude. The Ethiopian sorghum landrace collection was found to consist of 12 subpopulations with high levels of admixture (47%), representing all the major racial groups of cultivated sorghum with the exception of kafir. Redundancy analysis indicated that agroecology explained up to 10% of the total SNP variation, and geographical location up to 6%. GEA identified 18 significant SNP markers for environmental variables. These SNPs were found to be significantly enriched (P < 0.05) for a priori QTL for drought and cold adaptation. The findings from this study improve our understanding of the genetic control of adaptive traits in Ethiopian sorghum. Further, the Ethiopian sorghum germplasm collection provides sources of adaptation to harsh environments (cold and/or drought) that could be deployed in breeding programs globally for abiotic stress adaptation.
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Affiliation(s)
- T Menamo
- College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
| | - B Kassahun
- College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
| | - A K Borrell
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, University of Queensland, Warwick, QLD, 4370, Australia
| | - D R Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, University of Queensland, Warwick, QLD, 4370, Australia
| | - Y Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, University of Queensland, Warwick, QLD, 4370, Australia
| | - C Hunt
- Department of Agriculture and Fisheries, Hermitage Research Facility, Agri-Science Queensland, Warwick, QLD, 4370, Australia
| | - E Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), Hermitage Research Facility, University of Queensland, Warwick, QLD, 4370, Australia.
- Department of Agriculture and Fisheries, Hermitage Research Facility, Agri-Science Queensland, Warwick, QLD, 4370, Australia.
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22
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Genetic Analysis of Stem Diameter and Water Contents To Improve Sorghum Bioenergy Efficiency. G3-GENES GENOMES GENETICS 2020; 10:3991-4000. [PMID: 32907818 PMCID: PMC7642951 DOI: 10.1534/g3.120.401608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Biofuel made from agricultural products has the potential in contribute to a stable supply of fuel for growing energy demands. Some salient plant traits, such as stem diameter and water content, and their relationship to other important biomass-related traits are so far poorly understood. Here, we performed QTL mapping for three stem diameter and two water content traits in a S. bicolor BTx623 x IS3620c recombinant inbred line population of 399 genotypes, and validated the genomic regions identified using genome-wide association studies (GWAS) in a diversity panel of 354 accessions. The discovery of both co-localized and non-overlapping loci affecting stem diameter traits suggests that stem widths at different heights share some common genetic control, but also have some distinct genetic influences. Co-localizations of stem diameter and water content traits with other biomass traits including plant height, flowering time and the ‘dry’ trait, suggest that their inheritance may be linked functionally (pleiotropy) or physically (linkage disequilibrium). Water content QTL in homeologous regions resulting from an ancient duplication event may have been retained and continue to have related functions for an estimated 96 million years. Integration of QTL and GWAS data advanced knowledge of the genetic basis of stem diameter and water content components in sorghum, which may lead to tools and strategies for either enhancing or suppressing these traits, supporting advances toward improved quality of plant-based biomass for biofuel production.
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Kajiya-Kanegae H, Takanashi H, Fujimoto M, Ishimori M, Ohnishi N, Wacera W F, Omollo EA, Kobayashi M, Yano K, Nakano M, Kozuka T, Kusaba M, Iwata H, Tsutsumi N, Sakamoto W. RAD-seq-Based High-Density Linkage Map Construction and QTL Mapping of Biomass-Related Traits in Sorghum using the Japanese Landrace Takakibi NOG. PLANT & CELL PHYSIOLOGY 2020; 61:1262-1272. [PMID: 32353144 DOI: 10.1093/pcp/pcaa056] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
Sorghum [Sorghum bicolor (L.) Moench] grown locally by Japanese farmers is generically termed Takakibi, although its genetic diversity compared with geographically distant varieties or even within Takakibi lines remains unclear. To explore the genomic diversity and genetic traits controlling biomass and other physiological traits in Takakibi, we focused on a landrace, NOG, in this study. Admixture analysis of 460 sorghum accessions revealed that NOG belonged to the subgroup that represented Asian sorghums, and it was only distantly related to American/African accessions including BTx623. In an attempt to dissect major traits related to biomass, we generated a recombinant inbred line (RIL) from a cross between BTx623 and NOG, and we constructed a high-density linkage map based on 3,710 single-nucleotide polymorphisms obtained by restriction-site-associated DNA sequencing of 213 RIL individuals. Consequently, 13 fine quantitative trait loci (QTLs) were detected on chromosomes 2, 3, 6, 7, 8 and 9, which included five QTLs for days to heading, three for plant height (PH) and total shoot fresh weight and two for Brix. Furthermore, we identified two dominant loci for PH as being identical to the previously reported dw1 and dw3. Together, these results corroborate the diversified genome of Japanese Takakibi, while the RIL population and high-density linkage map generated in this study will be useful for dissecting other important traits in sorghum.
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Affiliation(s)
- Hiromi Kajiya-Kanegae
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8517, Japan
| | - Hideki Takanashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Masaru Fujimoto
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Motoyuki Ishimori
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Norikazu Ohnishi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046 Japan
| | - Fiona Wacera W
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046 Japan
| | - Everlyne A Omollo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046 Japan
| | - Masaaki Kobayashi
- Department of Life Sciences Faculty of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan
| | - Kentaro Yano
- Department of Life Sciences Faculty of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan
| | - Michiharu Nakano
- Graduate School of Integral Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526 Japan
| | - Toshiaki Kozuka
- Graduate School of Integral Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526 Japan
| | - Makoto Kusaba
- Graduate School of Integral Science for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526 Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Nobuhiro Tsutsumi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046 Japan
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Habyarimana E, Dall’Agata M, De Franceschi P, Baloch FS. Genome-wide association mapping of total antioxidant capacity, phenols, tannins, and flavonoids in a panel of Sorghum bicolor and S. bicolor × S. halepense populations using multi-locus models. PLoS One 2019; 14:e0225979. [PMID: 31805171 PMCID: PMC6894842 DOI: 10.1371/journal.pone.0225979] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/15/2019] [Indexed: 12/02/2022] Open
Abstract
Sorghum is widely used for producing food, feed, and biofuel, and it is increasingly grown to produce grains rich in health-promoting antioxidants. The conventional use of grain color as a proxy to indirectly select against or for antioxidants polyphenols in sorghum grain was hampered by the lack of consistency between grain color and the expected antioxidants concentration. Marker-assisted selection built upon significant loci identified through linkage disequilibrium studies showed interesting potential in several plant breeding and animal husbandry programs, and can be used in sorghum breeding for consumer-tailored antioxidant production. The purpose of this work was therefore to conduct genome-wide association study of sorghum grain antioxidants using single nucleotide polymorphisms in a novel diversity panel of Sorghum bicolor landraces and S. bicolor × S. halepense recombinant inbred lines. The recombinant inbred lines outperformed landraces for antioxidant production and contributed novel polymorphism. Antioxidant traits were highly correlated and showed very high broad-sense heritability. The genome-wide association analysis uncovered 96 associations 55 of which were major quantitative trait loci (QTLs) explaining 15 to 31% of the observed antioxidants variability. Eight major QTLs localized in novel chromosomal regions. Twenty-four pleiotropic major effect markers and two novel functional markers (Chr9_1550093, Chr10_50169631) were discovered. A novel pleiotropic major effect marker (Chr1_61095994) explained the highest proportion (R2 = 27–31%) of the variance observed in most traits evaluated in this work, and was in linkage disequilibrium with a hotspot of 19 putative glutathione S-transferase genes conjugating anthocyanins into vacuoles. On chromosome four, a hotspot region was observed involving major effect markers linked with putative MYB-bHLH-WD40 complex genes involved in the biosynthesis of the polyphenol class of flavonoids. The findings in this work are expected to help the scientific community particularly involved in marker assisted breeding for the development of sorghum cultivars with consumer-tailored antioxidants concentration.
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Affiliation(s)
- Ephrem Habyarimana
- CREA Research Center for Cereal and Industrial Crops, Bologna, Italy
- * E-mail:
| | | | | | - Faheem S. Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant Izzet Baysal University, Bolu, Turkey
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25
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Sorghum as a Novel Crop for Central Europe: Using a Broad Diversity Set to Dissect Temperate-Adaptation. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9090535] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Sorghum (Sorghum bicolor L. Moench) is a promising novel crop for Central Europe. However, enhancements in cold tolerance and early maturity are essential for a successful adaptation to cooler climates. We scored a broad sorghum diversity set (n = 338) for early chilling tolerance, high-latitude adaptation, and bioenergy related agronomical traits in multi-environment trials. Our results show a high phenotypic variation and medium to high heritabilities for most traits, indicating that a robust breeding progress is feasible. Several public accessions with a good adaptation to cooler climates were identified, which can serve as valuable base material for sorghum breeding in temperate areas. Genome-wide association studies reveal a polygenic (quantitative) character for most of the traits, confirming previous studies. Hence, for practical breeding, it will be difficult to conduct efficient marker-assisted selection for temperate-adaptation traits in genetically diverse material.
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26
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Khanal S, Dunne JC, Schwartz BM, Kim C, Milla-Lewis S, Raymer PL, Hanna WW, Adhikari J, Auckland SA, Rainville L, Paterson AH. Molecular Dissection of Quantitative Variation in Bermudagrass Hybrids ( Cynodon dactylon x transvaalensis): Morphological Traits. G3 (BETHESDA, MD.) 2019; 9:2581-2596. [PMID: 31208957 PMCID: PMC6686926 DOI: 10.1534/g3.119.400061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/05/2019] [Indexed: 11/30/2022]
Abstract
Bermudagrass (Cynodon (L.)) is the most important warm-season grass grown for forage or turf. It shows extensive variation in morphological characteristics and growth attributes, but the genetic basis of this variation is little understood. Detection and tagging of quantitative trait loci (QTL) affecting above-ground morphology with diagnostic DNA markers would provide a foundation for genetic and molecular breeding applications in bermudagrass. Here, we report early findings regarding genetic architecture of foliage (canopy height, HT), stolon (stolon internode length, ILEN and length of the longest stolon LLS), and leaf traits (leaf blade length, LLEN and leaf blade width, LW) in 110 F1 individuals derived from a cross between Cynodon dactylon (T89) and C. transvaalensis (T574). Separate and joint environment analyses were performed on trait data collected across two to five environments (locations, and/or years, or time), finding significant differences (P < 0.001) among the hybrid progeny for all traits. Analysis of marker-trait associations detected 74 QTL and 135 epistatic interactions. Composite interval mapping (CIM) and mixed-model CIM (MCIM) identified 32 main effect QTL (M-QTL) and 13 interacting QTL (int-QTL). Colocalization of QTL for plant morphology partially explained significant correlations among traits. M-QTL qILEN-3-2 (for ILEN; R2 = 11-19%), qLLS-7-1 (for LLS; R2 = 13-27%), qLEN-1-1 (for LLEN; R2 = 10-11%), and qLW-3-2 (for LW; R2 = 10-12%) were 'stable' across multiple environments, representing candidates for fine mapping and applied breeding applications. QTL correspondence between bermudagrass and divergent grass lineages suggests opportunities to accelerate progress by predictive breeding of bermudagrass.
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Affiliation(s)
- Sameer Khanal
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Jeffrey C Dunne
- Crop Science Department, North Carolina State University, Raleigh, NC 27695
| | - Brian M Schwartz
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA 31794, and
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Susana Milla-Lewis
- Crop Science Department, North Carolina State University, Raleigh, NC 27695
| | - Paul L Raymer
- Department of Crop and Soil Sciences, University of Georgia, Griffin, GA 30224
| | - Wayne W Hanna
- Department of Crop and Soil Sciences, University of Georgia, Tifton, GA 31794, and
| | - Jeevan Adhikari
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Susan A Auckland
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Lisa Rainville
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30606,
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27
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Genetic diversity and population structure of Ethiopian Capsicum germplasms. PLoS One 2019; 14:e0216886. [PMID: 31112575 PMCID: PMC6528999 DOI: 10.1371/journal.pone.0216886] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/30/2019] [Indexed: 11/19/2022] Open
Abstract
We established a collection of 142 Capsicum genotypes from different geographical areas of Ethiopia with the aim of capturing genetic diversity. Morphological traits and high-resolution melting analysis distinguished one Capsicum baccatum, nine Capsicum frutescens and 132 Capsicum annuum accessions in the collection. Measurement of plant growth parameters revealed variation between germplasms in parameters including plant height, stem thickness, internode length, number of side branches, fruit width, and fruit length. Broad-sense heritability was maximum for fruit weight, followed by length and width of leaves. We used genotyping by sequencing (GBS) to identify single-nucleotide polymorphisms (SNPs) in the panel of 142 Capsicum germplasms and found 2,831,791 genome-wide SNP markers. Among these, we selected 53,284 high-quality SNPs and used them to estimate the level of genetic diversity, population structure, and phylogenetic relationships. From model-based ancestry analysis, the phylogenetic tree and principal-coordinate analysis (PCoA), we identified two distinct genetic populations: one comprising 132 C. annuum accessions and the other comprising the nine C. frutescens accessions. GWAS analysis detected 509 SNP markers that were significantly associated with fruit-, stem- and leaf-related traits. This is the first comprehensive report of the analysis of genetic variation in Ethiopian Capsicum species involving a large number of accessions. The results will help breeders utilize the germplasm collection to improve existing commercial cultivars.
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Zhou Y, Srinivasan S, Mirnezami SV, Kusmec A, Fu Q, Attigala L, Salas Fernandez MG, Ganapathysubramanian B, Schnable PS. Semiautomated Feature Extraction from RGB Images for Sorghum Panicle Architecture GWAS. PLANT PHYSIOLOGY 2019; 179:24-37. [PMID: 30389784 PMCID: PMC6324233 DOI: 10.1104/pp.18.00974] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/21/2018] [Indexed: 05/20/2023]
Abstract
Because structural variation in the inflorescence architecture of cereal crops can influence yield, it is of interest to identify the genes responsible for this variation. However, the manual collection of inflorescence phenotypes can be time consuming for the large populations needed to conduct genome-wide association studies (GWAS) and is difficult for multidimensional traits such as volume. A semiautomated phenotyping pipeline, TIM (Toolkit for Inflorescence Measurement), was developed and used to extract unidimensional and multidimensional features from images of 1,064 sorghum (Sorghum bicolor) panicles from 272 genotypes comprising a subset of the Sorghum Association Panel. GWAS detected 35 unique single-nucleotide polymorphisms associated with variation in inflorescence architecture. The accuracy of the TIM pipeline is supported by the fact that several of these trait-associated single-nucleotide polymorphisms (TASs) are located within chromosomal regions associated with similar traits in previously published quantitative trait locus and GWAS analyses of sorghum. Additionally, sorghum homologs of maize (Zea mays) and rice (Oryza sativa) genes known to affect inflorescence architecture are enriched in the vicinities of TASs. Finally, our TASs are enriched within genomic regions that exhibit high levels of divergence between converted tropical lines and cultivars, consistent with the hypothesis that these chromosomal intervals were targets of selection during modern breeding.
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Affiliation(s)
- Yan Zhou
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
| | | | | | - Aaron Kusmec
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
| | - Qi Fu
- College of Agronomy, China Agricultural University, 100083 Beijing, China
| | | | | | | | - Patrick S Schnable
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
- College of Agronomy, China Agricultural University, 100083 Beijing, China
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Olatoye MO, Hu Z, Maina F, Morris GP. Genomic Signatures of Adaptation to a Precipitation Gradient in Nigerian Sorghum. G3 (BETHESDA, MD.) 2018; 8:3269-3281. [PMID: 30097471 PMCID: PMC6169398 DOI: 10.1534/g3.118.200551] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/04/2018] [Indexed: 02/05/2023]
Abstract
Evolution of plants under climatic gradients may lead to clinal adaptation. Understanding the genomic basis of clinal adaptation in crops species could facilitate breeding for climate resilience. We investigated signatures of clinal adaptation in the cereal crop sorghum (Sorghum bicolor L. [Moench]) to the precipitation gradient in West Africa using a panel (n = 607) of sorghum accessions from diverse agroclimatic zones of Nigeria. Significant correlations were observed between common-garden phenotypes of three putative climate-adaptive traits (flowering time, plant height, and panicle length) and climatic variables. The panel was characterized at >400,000 single nucleotide polymorphisms (SNPs) using genotyping-by-sequencing (GBS). Redundancy analysis indicated that a small proportion of SNP variation can be explained by climate (1%), space (1%), and climate collinear with space (3%). Discriminant analysis of principal components identified three genetic groups that are distributed differently along the precipitation gradient. Genome-wide association studies were conducted with phenotypes and three climatic variables (annual mean precipitation, precipitation in the driest quarter, and annual mean temperature). There was no overall enrichment of associations near a priori candidate genes implicated in flowering time, height, and inflorescence architecture in cereals, but several significant associations were found near a priori candidates including photoperiodic flowering regulators SbCN12 and Ma6 Together, the findings suggest that a small (3%) but significant proportion of nucleotide variation in Nigerian sorghum landraces reflects clinal adaptation along the West African precipitation gradient.
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Affiliation(s)
- Marcus O Olatoye
- Department of Agronomy, Kansas State University, Manhattan KS 66506
| | - Zhenbin Hu
- Department of Agronomy, Kansas State University, Manhattan KS 66506
| | - Fanna Maina
- Department of Agronomy, Kansas State University, Manhattan KS 66506
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Spindel JE, Dahlberg J, Colgan M, Hollingsworth J, Sievert J, Staggenborg SH, Hutmacher R, Jansson C, Vogel JP. Association mapping by aerial drone reveals 213 genetic associations for Sorghum bicolor biomass traits under drought. BMC Genomics 2018; 19:679. [PMID: 30223789 PMCID: PMC6142696 DOI: 10.1186/s12864-018-5055-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/04/2018] [Indexed: 11/10/2022] Open
Abstract
Background Sorghum bicolor is the fifth most commonly grown cereal worldwide and is remarkable for its drought and abiotic stress tolerance. For these reasons and the large size of biomass varieties, it has been proposed as a bioenergy crop. However, little is known about the genes underlying sorghum’s abiotic stress tolerance and biomass yield. Results To uncover the genetic basis of drought tolerance in sorghum at a genome-wide level, we undertook a high-density phenomics genome wide association study (GWAS) in which 648 diverse sorghum lines were phenotyped at two locations in California once per week by drone over the course of a growing season. Biomass, height, and leaf area were measured by drone for individual field plots, subjected to two drought treatments and a well-watered control. The resulting dataset of ~ 171,000 phenotypic data-points was analyzed along with 183,989 genotype by sequence markers to reveal 213 high-quality, replicated, and conserved GWAS associations. Conclusions The genomic intervals defined by the associations include many strong candidate genes, including those encoding heat shock proteins, antifreeze proteins, and other domains recognized as important to plant stress responses. The markers identified by our study can be used for marker assisted selection for drought tolerance and biomass. In addition, our results are a significant step toward identifying specific sorghum genes controlling drought tolerance and biomass yield. Electronic supplementary material The online version of this article (10.1186/s12864-018-5055-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer E Spindel
- DOE Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA, 94598, USA.,Present Address: Monsanto, St. Louis, MO, USA
| | - Jeffery Dahlberg
- UC-ANR Kearney Agricultural Research and Extension Center, 9240 S Riverbend Ave, Parlier, CA, 93648, USA
| | - Matthew Colgan
- Blue River Technology, 575 N Pastoria Ave, Sunnyvale, CA, 94085, USA
| | - Joy Hollingsworth
- UC-ANR Kearney Agricultural Research and Extension Center, 9240 S Riverbend Ave, Parlier, CA, 93648, USA
| | - Julie Sievert
- UC-ANR Kearney Agricultural Research and Extension Center, 9240 S Riverbend Ave, Parlier, CA, 93648, USA
| | | | - Robert Hutmacher
- UC-ANR West Side Research & Extension Center, 17353 W Oakland Ave, Five Points, CA, 93624, USA
| | - Christer Jansson
- Pacific Northwest National Laboratory: Environmental Molecular Sciences Laboratory, 902 Battelle Blvd, Richland, WA, 99354, USA
| | - John P Vogel
- DOE Joint Genome Institute, 2800 Mitchell Dr, Walnut Creek, CA, 94598, USA.
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Ge C, Ai X, Jia S, Yang Y, Che L, Yi Z, Chen C. Interspecific genetic maps in Miscanthus floridulus and M. sacchariflorus accelerate detection of QTLs associated with plant height and inflorescence. Mol Genet Genomics 2018; 294:35-45. [PMID: 30159617 DOI: 10.1007/s00438-018-1486-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/23/2018] [Indexed: 12/26/2022]
Abstract
Miscanthus is recognized as a promising lignocellulosic crop for the production of bioethanol and bioproducts worldwide. To facilitate the identification of agronomical important traits and establish genetics knowledge, two genetic maps were developed from a controlled interspecific cross between M. floridulus and M. sacchariflorus. A total of 650 SSR markers were mapped in M. floridulus, spanning 19 linkage groups and 2053.31 cM with an average interval of 3.25 cM. The map of M. sacchariflorus comprised 495 SSR markers in 19 linkage groups covering 1684.86 cM with an average interval of 3.54 cM. The estimation on genome length indicated that the genome coverage of parental genetic maps were 93.87% and 89.91%, respectively. Eighty-eight bi-parental common markers were allowed to connect the two maps, and six pairs of syntenic linkage groups were recognized. Furthermore, quantitative trait loci (QTL) mapping of three agronomic traits, namely, plant height (PH), heading time (HT), and flowering time (FT), demonstrated that a total of 66 QTLs were identified in four consecutive years using interval mapping and multiple-QTL model. The LOD value of these QTLs ranged from 2.51 to 10.60, and the phenotypic variation explained varied from 9.50 to 37.10%. QTL cluster in syntenic groups MF19/MS7 contained six stable QTLs associated with PH, HT, and FT. In conclusion, we report for the first time the genetic mapping of biomass traits in M. floridulus and M. sacchariflorus. These results will be a valuable genetic resource, facilitating the discovery of essential genes and breeding of Miscanthus.
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Affiliation(s)
- Chunxia Ge
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, Shandong, China.,College of Agronomy, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Xin Ai
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Shengfeng Jia
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, Shandong, China.,College of Agronomy, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Yinqing Yang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, Shandong, China.,College of Agronomy, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Lu Che
- Network Information Technology Center, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Zili Yi
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Cuixia Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, Shandong, China. .,College of Agronomy, Shandong Agricultural University, Taian, 271018, Shandong, China.
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Genotyping by Sequencing of 393 Sorghum bicolor BTx623 × IS3620C Recombinant Inbred Lines Improves Sensitivity and Resolution of QTL Detection. G3-GENES GENOMES GENETICS 2018; 8:2563-2572. [PMID: 29853656 PMCID: PMC6071585 DOI: 10.1534/g3.118.200173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We describe a genetic map with a total of 381 bins of 616 genotyping by sequencing (GBS)-based SNP markers in a F6-F8 recombinant inbred line (RIL) population of 393 individuals derived from crossing S. bicolor BTx623 to S. bicolor IS3620C, a guinea line substantially diverged from BTx623. Five segregation distorted regions were found with four showing enrichment for S. bicolor alleles, suggesting possible selection during formation of this RIL population. A quantitative trait locus (QTL) study with this number of individuals, tripled relative to prior studies of this cross, provided resources, validated previous findings, and demonstrated improved power to detect plant height and flowering time related QTL relative to other published studies. An unexpected low correlation between flowering time and plant height permitted us to separate QTL for each trait and provide evidence against pleiotropy. Ten non- random syntenic regions conferring QTL for the same trait suggest that those QTL may represent alleles at genes functioning in the same manner since the 96 million year ago genome duplication that created these syntenic relationships, while syntenic regions conferring QTL for different trait may suggest sub-functionalization after duplication. Collectively, this study provides resources for marker-assisted breeding, as well as a framework for fine mapping and subsequent cloning of major genes for important traits such as plant height and flowering time in sorghum.
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Salas Fernandez MG, Bao Y, Tang L, Schnable PS. A High-Throughput, Field-Based Phenotyping Technology for Tall Biomass Crops. PLANT PHYSIOLOGY 2017; 174:2008-2022. [PMID: 28620124 PMCID: PMC5543940 DOI: 10.1104/pp.17.00707] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 06/13/2017] [Indexed: 05/18/2023]
Abstract
Recent advances in omics technologies have not been accompanied by equally efficient, cost-effective, and accurate phenotyping methods required to dissect the genetic architecture of complex traits. Even though high-throughput phenotyping platforms have been developed for controlled environments, field-based aerial and ground technologies have only been designed and deployed for short-stature crops. Therefore, we developed and tested Phenobot 1.0, an auto-steered and self-propelled field-based high-throughput phenotyping platform for tall dense canopy crops, such as sorghum (Sorghum bicolor). Phenobot 1.0 was equipped with laterally positioned and vertically stacked stereo RGB cameras. Images collected from 307 diverse sorghum lines were reconstructed in 3D for feature extraction. User interfaces were developed, and multiple algorithms were evaluated for their accuracy in estimating plant height and stem diameter. Tested feature extraction methods included the following: (1) User-interactive Individual Plant Height Extraction (UsIn-PHe) based on dense stereo three-dimensional reconstruction; (2) Automatic Hedge-based Plant Height Extraction (Auto-PHe) based on dense stereo 3D reconstruction; (3) User-interactive Dense Stereo Matching Stem Diameter Extraction; and (4) User-interactive Image Patch Stereo Matching Stem Diameter Extraction (IPaS-Di). Comparative genome-wide association analysis and ground-truth validation demonstrated that both UsIn-PHe and Auto-PHe were accurate methods to estimate plant height, while Auto-PHe had the additional advantage of being a completely automated process. For stem diameter, IPaS-Di generated the most accurate estimates of this biomass-related architectural trait. In summary, our technology was proven robust to obtain ground-based high-throughput plant architecture parameters of sorghum, a tall and densely planted crop species.
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Affiliation(s)
| | - Yin Bao
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa 50011
| | - Lie Tang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa 50011
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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: 85] [Impact Index Per Article: 12.1] [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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35
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Zu P, Schiestl FP. The effects of becoming taller: direct and pleiotropic effects of artificial selection on plant height in Brassica rapa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:1009-1019. [PMID: 27889935 DOI: 10.1111/tpj.13440] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/07/2016] [Accepted: 11/18/2016] [Indexed: 06/06/2023]
Abstract
Plant height is an important trait for plant reproductive success. Plant height is often under pollinator-mediated selection, and has been shown to be correlated with various other traits. However, few studies have examined the evolutionary trajectory of plant height under selection and the pleiotropic effects of plant height evolution. We conducted a bi-directional artificial selection experiment on plant height with fast cycling Brassica rapa plants to estimate its heritability and genetic correlations, and to reveal evolutionary responses to artificial selection on height and various correlated traits. With the divergent lines obtained through artificial selection, we subsequently conducted pollinator-choice assays and investigated resource limitation of fruit production. We found that plant height variation is strongly genetically controlled (with a realized heritability of 41-59%). Thus, plant height can evolve rapidly under phenotypic selection. In addition, we found remarkable pleiotropic effects in phenology, morphology, floral scent, color, nectar and leaf glucosinolates. Most traits were increased in tall-line plants, but flower size, UV reflection and glucosinolates were decreased, indicating potential trade-offs. Pollinators preferred plants of the tall selection lines over the short selection lines in both greenhouse experiments with bumblebees and field experiment with natural pollinators. We did not detect any differences in resource limitation between plants of the different selection lines. Overall, our study predicts that increased height should evolve under positive pollinator-mediated directional selection with potential trade-offs in floral signals and herbivore defense.
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Affiliation(s)
- Pengjuan Zu
- Department of Systematic and Evolutionary Botany, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
| | - Florian P Schiestl
- Department of Systematic and Evolutionary Botany, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
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36
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Cuevas HE, Rosa-Valentin G, Hayes CM, Rooney WL, Hoffmann L. Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement. BMC Genomics 2017; 18:108. [PMID: 28125967 PMCID: PMC5270221 DOI: 10.1186/s12864-016-3475-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/26/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The USDA Agriculture Research Service National Plant Germplasm System (NPGS) preserves the largest sorghum germplasm collection in the world, which includes 7,217 accessions from the center of diversity in Ethiopia. The characterization of this exotic germplasm at a genome-wide scale will improve conservation efforts and its utilization in research and breeding programs. Therefore, we phenotyped a representative core set of 374 Ethiopian accessions at two locations for agronomic traits and characterized the genomes. RESULTS Using genotyping-by-sequencing, we identified 148,476 single-nucleotide polymorphism (SNP) markers distributed across the entire genome. Over half of the alleles were rare (frequency < 0.05). The genetic profile of each accession was unique (i.e., no duplicates), and the average genetic distance among accessions was 0.70. Based on population structure and cluster analyses, we separated the collection into 11 populations with pairwise F ST values ranging from 0.11 to 0.47. In total, 198 accessions (53%) were assigned to one of these populations with an ancestry membership coefficient of larger than 0.60; these covered 90% of the total genomic variation. We characterized these populations based on agronomic and seed compositional traits. We performed a cluster analysis with the sorghum association panel based on 26,026 SNPs and determined that nine of the Ethiopian populations expanded the genetic diversity in the panel. Genome-wide association analysis demonstrated that these low-coverage data and the observed population structure could be employed for the genomic dissection of important phenotypes in this core set of Ethiopian sorghum germplasm. CONCLUSIONS The NPGS Ethiopian sorghum germplasm is a genetically and phenotypically diverse collection comprising 11 populations with high levels of admixture. Genetic associations with agronomic traits can be used to improve the screening of exotic germplasm for selection of specific populations. We detected many rare alleles, suggesting that this germplasm contains potentially useful undiscovered alleles, but their discovery and characterization will require extensive effort. The genotypic data available for these accessions provide a valuable resource for sorghum breeders and geneticists to effectively improve crops.
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Affiliation(s)
- Hugo E Cuevas
- USDA-ARS, Tropical Agriculture Research Station, 2200 Pedro Albizu Campos Avenue, Mayaguez, 00680, Puerto Rico.
| | - Giseiry Rosa-Valentin
- USDA-ARS, Tropical Agriculture Research Station, 2200 Pedro Albizu Campos Avenue, Mayaguez, 00680, Puerto Rico
| | - Chad M Hayes
- USDA-ARS, Cropping Systems Research Laboratory, 3810 4th Street, Lubbock, TX, 79415, USA
| | - William L Rooney
- Departments of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA
| | - Leo Hoffmann
- Departments of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA
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Lu Q, Niu X, Zhang M, Wang C, Xu Q, Feng Y, Yang Y, Wang S, Yuan X, Yu H, Wang Y, Chen X, Liang X, Wei X. Genome-Wide Association Study of Seed Dormancy and the Genomic Consequences of Improvement Footprints in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2017; 8:2213. [PMID: 29354150 PMCID: PMC5760558 DOI: 10.3389/fpls.2017.02213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/18/2017] [Indexed: 05/03/2023]
Abstract
Seed dormancy is an important agronomic trait affecting grain yield and quality because of pre-harvest germination and is influenced by both environmental and genetic factors. However, our knowledge of the factors controlling seed dormancy remains limited. To better reveal the molecular mechanism underlying this trait, a genome-wide association study was conducted in an indica-only population consisting of 453 accessions genotyped using 5,291 SNPs. Nine known and new significant SNPs were identified on eight chromosomes. These lead SNPs explained 34.9% of the phenotypic variation, and four of them were designed as dCAPS markers in the hope of accelerating molecular breeding. Moreover, a total of 212 candidate genes was predicted and eight candidate genes showed plant tissue-specific expression in expression profile data from different public bioinformatics databases. In particular, LOC_Os03g10110, which had a maize homolog involved in embryo development, was identified as a candidate regulator for further biological function investigations. Additionally, a polymorphism information content ratio method was used to screen improvement footprints and 27 selective sweeps were identified, most of which harbored domestication-related genes. Further studies suggested that three significant SNPs were adjacent to the candidate selection signals, supporting the accuracy of our genome-wide association study (GWAS) results. These findings show that genome-wide screening for selective sweeps can be used to identify new improvement-related DNA regions, although the phenotypes are unknown. This study enhances our knowledge of the genetic variation in seed dormancy, and the new dormancy-associated SNPs will provide real benefits in molecular breeding.
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Affiliation(s)
- Qing Lu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement and Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Xiaojun Niu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Mengchen Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Caihong Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qun Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yue Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yaolong Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Shan Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiaoping Yuan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Hanyong Yu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yiping Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement and Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement and Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, China
| | - Xinghua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- *Correspondence: Xinghua Wei
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CSGRqtl: A Comparative Quantitative Trait Locus Database for Saccharinae Grasses. Methods Mol Biol 2016. [PMID: 27987176 DOI: 10.1007/978-1-4939-6658-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Conventional biparental quantitative trait locus (QTL) mapping has led to some successes in the identification of causal genes in many organisms. QTL likelihood intervals not only provide "prior information" for finer-resolution approaches such as GWAS but also provide better statistical power than GWAS to detect variants with low/rare frequency in a natural population. Here, we describe a new element of an ongoing effort to provide online resources to facilitate study and improvement of the important Saccharinae clade. The primary goal of this new resource is the anchoring of published QTLs for this clade to the Sorghum genome. Genetic map alignments translate a wealth of genomic information from sorghum to Saccharum spp., Miscanthus spp., and other taxa. In addition, genome alignments facilitate comparison of the Saccharinae QTL sets to those of other taxa that enjoy comparable resources, exemplified herein by rice.
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Wolabu TW, Tadege M. Photoperiod response and floral transition in sorghum. PLANT SIGNALING & BEHAVIOR 2016; 11:e1261232. [PMID: 27854155 PMCID: PMC5225928 DOI: 10.1080/15592324.2016.1261232] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 11/11/2016] [Indexed: 05/13/2023]
Abstract
Sorghum is a short day plant with strong photoperiod response and its cultivation for grain in temperate regions necessitated the development of photoperiod insensitive mutants that can flower rapidly in the long days of summer. Wild type genotypes grow vegetatively in summer accumulating significant biomass before floral transition ensues during the shorter days of fall. Thus, photoperiod insensitive mutants are grown for grain production while photoperiod sensitive wild type genotypes are grown for forage and biomass feedstock production in the United States. However, the molecular mechanism of photoperiod response and floral transition is poorly understood in sorghum. We have previously reported 3 FLOWERING LOCUS T homologues (SbFT1, SbFT8 and SbFT10) that serve as the ultimate mediators of photoperiod response and floral transition, but more work remains to be done to clearly define the molecular function of the upstream regulatory factors. One of the major QTL that accounts for 85% of the flowering time variation, which was reported to be encoding the PRR37 protein is now debated to be encoding the SbFT12 protein, raising further questions as to how SbFT12 may regulate sorghum florigens. Further molecular analyses will uncover the true nature of the day length sensors in sorghum and the mechanisms of their interactions with florigens to modulate photoperiod dependent vegetative growth and floral transition.
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Affiliation(s)
- Tezera W. Wolabu
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, USA
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, OK, USA
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Nimmakayala P, Abburi VL, Saminathan T, Alaparthi SB, Almeida A, Davenport B, Nadimi M, Davidson J, Tonapi K, Yadav L, Malkaram S, Vajja G, Hankins G, Harris R, Park M, Choi D, Stommel J, Reddy UK. Genome-wide Diversity and Association Mapping for Capsaicinoids and Fruit Weight in Capsicum annuum L. Sci Rep 2016; 6:38081. [PMID: 27901114 PMCID: PMC5128918 DOI: 10.1038/srep38081] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/03/2016] [Indexed: 12/24/2022] Open
Abstract
Accumulated capsaicinoid content and increased fruit size are traits resulting from Capsicum annuum domestication. In this study, we used a diverse collection of C. annuum to generate 66,960 SNPs using genotyping by sequencing. The study identified 1189 haplotypes containing 3413 SNPs. Length of individual linkage disequilibrium (LD) blocks varied along chromosomes, with regions of high and low LD interspersed with an average LD of 139 kb. Principal component analysis (PCA), Bayesian model based population structure analysis and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions are in agreement with capsaicin content (CA) and fruit weight (FW) classifications indicating the importance of these traits in shaping modern pepper genome. PCA and IBS were used in a mixed linear model of capsaicin and dihydrocapsaicin content and fruit weight to reduce spurious associations because of confounding effects of subpopulations in genome-wide association study (GWAS). Our GWAS results showed SNPs in Ankyrin-like protein, IKI3 family protein, ABC transporter G family and pentatricopeptide repeat protein are the major markers for capsaicinoids and of 16 SNPs strongly associated with FW in both years of the study, 7 are located in known fruit weight controlling genes.
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Affiliation(s)
- Padma Nimmakayala
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Venkata L Abburi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Thangasamy Saminathan
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Suresh B Alaparthi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Aldo Almeida
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Brittany Davenport
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Marjan Nadimi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Joshua Davidson
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Krittika Tonapi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Lav Yadav
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Sridhar Malkaram
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Gopinath Vajja
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Gerald Hankins
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Robert Harris
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
| | - Minkyu Park
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-321, Republic of Korea
| | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-321, Republic of Korea
| | - John Stommel
- Genetic Improvement of Fruits and Vegetables Laboratory (USDA, ARS), Beltsville, MD-20705, USA
| | - Umesh K Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV-25112, USA
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Mauro-Herrera M, Doust AN. Development and Genetic Control of Plant Architecture and Biomass in the Panicoid Grass, Setaria. PLoS One 2016; 11:e0151346. [PMID: 26985990 PMCID: PMC4795695 DOI: 10.1371/journal.pone.0151346] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/05/2016] [Indexed: 01/12/2023] Open
Abstract
The architecture of a plant affects its ability to compete for light and to respond to environmental stresses, thus affecting overall fitness and productivity. Two components of architecture, branching and height, were studied in 182 F7 recombinant inbred lines (RILs) at the vegetative, flowering and mature developmental stages in the panicoid C4 model grass system, Setaria. The RIL population was derived from a cross between domesticated S. italica (foxtail millet) and its wild relative S. viridis (green foxtail). In both field and greenhouse trials the wild parent was taller initially, started branching earlier, and flowered earlier, while the domesticated parent was shorter initially, but flowered later, producing a robust tall plant architecture with more nodes and leaves on the main culm and few or no branches. Biomass was highly correlated with height of the plant and number of nodes on the main culm, and generally showed a negative relationship with branch number. However, several of the RILs with the highest biomass in both trials were significantly more branched than the domesticated parent of the cross. Quantitative trait loci (QTL) analyses indicate that both height and branching are controlled by multiple genetic regions, often with QTL for both traits colocalizing in the same genomic regions. Genomic positions of several QTL colocalize with QTL in syntenic regions in other species and contain genes known to control branching and height in sorghum, maize, and switchgrass. Included in these is the ortholog of the rice SD-1 semi-dwarfing gene, which underlies one of the major Setaria height QTL. Understanding the relationships between height and branching patterns in Setaria, and their genetic control, is an important step to gaining a comprehensive knowledge of the development and genetic regulation of panicoid grass architecture.
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Affiliation(s)
- Margarita Mauro-Herrera
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK 74078, United States of America
| | - Andrew N. Doust
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK 74078, United States of America
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