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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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Lee JS, Bae SJ, Kim JS, Kim C, Kang BC. A streamlined guide RNA screening system for genome editing in Sorghum bicolor. PLANT METHODS 2023; 19:90. [PMID: 37633915 PMCID: PMC10463630 DOI: 10.1186/s13007-023-01058-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 07/18/2023] [Indexed: 08/28/2023]
Abstract
BACKGROUND Genome editing tools derived from clustered regularly interspaced short palindromic repeats (CRISPR) systems have been developed for generating targeted mutations in plants. Although these tools hold promise for rapid crop improvement, target-specific guide RNAs exhibit variable activity. To improve genome editing, a rapid and precise method for evaluating their efficiency is necessary. RESULTS Here we report an efficient system for screening single guide RNAs (sgRNAs) for genome editing in sorghum using a transient protoplast transfection assay. Protoplasts were isolated from leaves from sorghum plants cultivated under three different conditions. Cultivation for three days of continuous darkness following seven days with a 16-h light and 8-h dark photoperiod resulted in the highest yield of viable protoplasts and the highest protoplast transfection efficiency. We tested both plasmid-mediated and ribonucleoprotein-based delivery to protoplasts, via polyethylene glycol-mediated transfection, of CRISPR components targeting the sorghum genome. The frequencies of small insertions and deletions induced by a set of sgRNAs targeting four endogenous sorghum genes were analyzed via targeted deep sequencing. Our screening system induced indels in sorghum protoplasts at frequencies of up to 77.8% (plasmid) and 18.5% (RNP). The entire screening system was completed within 16 days. CONCLUSIONS The screening system optimized in this study for predicting sgRNA activity for genome editing in sorghum is efficient and straightforward. This system will reduce the time and effort needed for sorghum genome editing.
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Affiliation(s)
- Jeong Sun Lee
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon, Republic of Korea
- National Research Safety Headquarters, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Republic of Korea
| | - Su-Ji Bae
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea
| | - Jin-Soo Kim
- NUS Synthetic Biology for Clinical & Technological Innovation (SynCTI) and Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Changsoo Kim
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon, Republic of Korea.
| | - Beum-Chang Kang
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea.
- Department of Horticulture, College of Agricultural Life Science, Jeonbuk National University, Jeonju, Republic of Korea.
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Wenndt A, Boyles R, Ackerman A, Sapkota S, Repka A, Nelson R. Host Determinants of Fungal Species Composition and Symptom Manifestation in the Sorghum Grain Mold Disease Complex. PLANT DISEASE 2023; 107:315-325. [PMID: 36800304 DOI: 10.1094/pdis-03-22-0675-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Sorghum grain mold (SGM) is an important multifungal disease complex affecting sorghum (Sorghum bicolor) production systems worldwide. SGM-affected sorghum grain can be contaminated with potent fumonisin mycotoxins produced by Fusarium verticillioides, a prevalent SGM-associated taxon. Historically, efforts to improve resistance to SGM have achieved only limited success. Classical approaches to evaluating SGM resistance are based solely on disease severity, which offers little insight regarding the distinct symptom manifestations within the disease complex. In this study, three novel phenotypes were developed to facilitate assessment of SGM symptom manifestation. A sorghum diversity panel composed of 390 accessions was inoculated with endogenous strains of F. verticillioides and evaluated for these phenotypes, as well as for the conventional panicle grain mold severity rating phenotype, in South Carolina, U.S.A., in 2017 and 2019. Distributions of phenotype values were examined, broad-sense heritability was estimated, and relationships to botanical race were explored. A typology of SGM symptom manifestations was developed to classify accessions using principal component analysis and k-means clustering, constituting a novel option for basing breeding decisions on SGM outcomes more nuanced than disease severity. Genome-wide association studies were performed using SGM trait data, resulting in the identification of 19 significant single nucleotide polymorphisms in linkage disequilibrium with a total of 86 gene models. Our findings provide a basis of exploratory evidence regarding the genetic architecture of SGM symptom manifestation and indicate that traits other than disease severity could be tractable targets for SGM resistance breeding.
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Affiliation(s)
- Anthony Wenndt
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Richard Boyles
- Plant and Environmental Sciences, Pee Dee Research and Education Center, Clemson University, Florence, SC 29506
| | - Arlyn Ackerman
- Plant and Environmental Sciences, Pee Dee Research and Education Center, Clemson University, Florence, SC 29506
| | - Sirjan Sapkota
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634
| | - Ace Repka
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Rebecca Nelson
- Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
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Hudzenko VM, Polishchuk TP, Lysenko AA, Fedorenko IV, Fedorenko MV, Khudolii LV, Ishchenko VA, Kozelets HM, Babenko AI, Tanchyk SP, Mandrovska SM. Elucidation of gene action and combining ability for productive tillering in spring barley. REGULATORY MECHANISMS IN BIOSYSTEMS 2022. [DOI: 10.15421/022225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The purpose of the present study is to identify breeding and genetic peculiarities for productive tillering in spring barley genotypes of different origin, purposes of usage and botanical affiliation, as well as to identify effective genetic sources to further improving of the trait. There were created two complete (6 × 6) diallel crossing schemes. Into the Scheme I elite Ukrainian (MIP Tytul and Avhur) and Western European (Datcha, Quench, Gladys, and Beatrix) malting spring barley varieties were involved. Scheme II included awnless covered barley varieties Kozyr and Vitrazh bred at the Plant Production Institute named after V. Y. Yuriev of NAAS of Ukraine, naked barley varieties Condor and CDC Rattan from Canada, as well as awned feed barley variety MIP Myroslav created at MIW and malting barley variety Sebastian from Denmark. For more reliable and informative characterization of barley varieties and their progeny for productive tillering in terms of inheritance, parameters of genetic variation and general combining ability (GCA) statistical analyses of experimental data from different (2019 and 2020) growing seasons were conducted. Accordingly to the indicator of phenotypic dominance all possible modes of inheritance were detected, except for negative dominance in the Scheme I in 2020. The degree of phenotypic dominance significantly varied depending on both varieties involved in crossing schemes and conditions of the years of trials. There was overdominance in loci in both schemes in both years. The other parameters of genetic variation showed significant differences in gene action for productive tillering between crossing Schemes. In Scheme I in both years the dominance was mainly unidirectional and due to dominant effects. In the Scheme II in both years there was multidirectional dominance. In Scheme I compliance with the additive-dominant system was revealed in 2019, but in 2020 there was a strong epistasis. In Scheme II in both years non-allelic interaction was identified. In general, the mode of gene action showed a very complex gene action for productive tillering in barley and a significant role of non-genetic factors in phenotypic manifestation of the trait. Despite this, the level of heritability in the narrow sense in both Schemes pointed to the possibility of the successful selection of individuals with genetically determined increased productive tillering in the splitting generations. In Scheme I the final selection for productive tillering will be more effective in later generations, when dominant alleles become homozygous. In Scheme II it is theoretically possible to select plants with high productive tillering on both recessive and dominant basis. In both schemes the non-allelic interaction should be taken into consideration. Spring barley varieties Beatrix, Datcha, MIP Myroslav and Kozyr can be used as effective genetic sources for involvement in crossings aimed at improving the productive tillering. The results of present study contribute to further development of studies devoted to evaluation of gene action for yield-related traits in spring barley, as well as identification of new genetic sources for plant improvement.
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Low-Intensity, High-Frequency Grazing Strategy Increases Herbage Production and Beef Cattle Performance on Sorghum Pastures. Animals (Basel) 2021; 12:ani12010013. [PMID: 35011119 PMCID: PMC8749659 DOI: 10.3390/ani12010013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/04/2022] Open
Abstract
Simple Summary Finding smart management targets to improve livestock production and make it sustainable are very important for livestock in the tropics. We assessed the effects of high-intensity and low-frequency (HILF) vs. low-intensity and high-frequency (LIHF) grazing on herbage production and performance of beef cattle grazing sorghum pastures. The LIHF resulted in shorter rest periods when compared with the HILF. The greater leaf lamina mass in LIHF allowed greater sward light interception at post-grazing, resulting in greater total herbage production than HILF. The average daily gain (ADG) was greater for the LIHF than for the HILF treatment; however, even with a greater stocking rate in the HILF, there was no difference for LW gain per ha. Our findings demonstrated that the LIHF strategy that is based on offering to the animals an optimal sward structure to favor the herbage intake rate fosters greater herbage production, harvesting efficiency, and ADG without compromising LW gain per area, despite the lower herbage harvested per stocking cycle. Therefore, we conclude that the classic trade-off between animal performance and forage production could be offset on tropical grasses grazed by beef cattle only by adjusting grazing management according to a LIHF grazing management strategy. Abstract We assessed the effects of high-intensity and low-frequency (HILF) vs. low-intensity and high-frequency (LIHF) grazing on herbage production and performance of beef cattle grazing sorghum pastures. The experimental design was a complete randomized block with two treatments and four replicates (paddocks), carried out in 2014/15. The management target of 50 and 30 cm for pre- and post-grazing, respectively, a LIHF grazing management strategy oriented to maximize beef cattle herbage intake per unit time, was compared with a HILF grazing management strategy of 80 and 20 cm for pre- and post-grazing, respectively, aiming to maximize herbage accumulation and harvest efficiency. Sixteen Brangus steers of 15-month-old and 265 ± 21 kg of live weight (LW) were randomly distributed to paddocks (experimental units). The LIHF resulted in shorter rest periods when compared with the HILF. The greater leaf lamina mass in LIHF allowed greater sward light interception at post-grazing, resulting in greater total herbage production than HILF (7581 and 4154 kg DM/ha, respectively). The average daily gain (ADG) of steers was greater for the LIHF than for the HILF treatment (0.950 and 0.702 kg/animal, respectively); however, even with a greater stocking rate in the HILF, there was no difference for LW gain per ha, with an average of 4 kg LW/ha/day. Our findings demonstrated that the LIHF strategy that is based on offering to the animals an optimal sward structure to favor the maximum herbage intake rate fosters greater herbage production, harvesting efficiency, and ADG without compromising LW gain per area of beef steers, despite the lower herbage harvested per stocking cycle.
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6
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Bai Y, Zhao X, Yao X, Yao Y, An L, Li X, Wang Y, Gao X, Jia Y, Guan L, Li M, Wu K, Wang Z. Genome wide association study of plant height and tiller number in hulless barley. PLoS One 2021; 16:e0260723. [PMID: 34855842 PMCID: PMC8639095 DOI: 10.1371/journal.pone.0260723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/15/2021] [Indexed: 11/18/2022] Open
Abstract
Hulless barley (Hordeum vulgare L. var. nudum), also called naked barley, is a unique variety of cultivated barley. The genome-wide specific length amplified fragment sequencing (SLAF-seq) method is a rapid deep sequencing technology that is used for the selection and identification of genetic loci or markers. In this study, we collected 300 hulless barley accessions and used the SLAF-seq method to identify candidate genes involved in plant height (PH) and tiller number (TN). We obtained a total of 1407 M paired-end reads, and 228,227 SLAF tags were developed. After filtering using an integrity threshold of >0.8 and a minor allele frequency of >0.05, 14,504,892 single-nucleotide polymorphisms (SNP) loci were screened out. The remaining SNPs were used for the construction of a neighbour-joining phylogenetic tree, and the three subcluster members showed no obvious differentiation among regional varieties. We used a genome wide association study approach to identify 1006 and 113 SNPs associated with TN and PH, respectively. Based on best linear unbiased predictors (BLUP), 41 and 29 SNPs associated with TN and PH, respectively. Thus, several of genes, including Hd3a and CKX5, may be useful candidates for the future genetic breeding of hulless barley. Taken together, our results provide insight into the molecular mechanisms controlling barley architecture, which is important for breeding and yield.
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Affiliation(s)
- Yixiong Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
| | - Xiaohong Zhao
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
- Good Agricultural Practices Research Center of Traditional, Chongqing Institute of Medicinal Plant Cultivation, Chongqing, China
| | - Xiaohua Yao
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
| | - Youhua Yao
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
| | - Likun An
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
| | - Xin Li
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
| | - Yong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Xin Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Yatao Jia
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Lulu Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Man Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Kunlun Wu
- Qinghai University, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, Qinghai Province, China
- * E-mail: (KW); (ZW)
| | - Zhonghua Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail: (KW); (ZW)
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7
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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
- * E-mail:
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8
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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: 11] [Impact Index Per Article: 3.7] [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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9
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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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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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11
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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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12
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Zhu Y, Wagner D. Plant Inflorescence Architecture: The Formation, Activity, and Fate of Axillary Meristems. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a034652. [PMID: 31308142 DOI: 10.1101/cshperspect.a034652] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The above-ground plant body in different plant species can have very distinct forms or architectures that arise by recurrent redeployment of a finite set of building blocks-leaves with axillary meristems, stems or branches, and flowers. The unique architectures of plant inflorescences in different plant families and species, on which this review focuses, determine the reproductive success and yield of wild and cultivated plants. Major contributors to the inflorescence architecture are the activity and developmental trajectories adopted by axillary meristems, which determine the degree of branching and the number of flowers formed. Recent advances in genetic and molecular analyses in diverse flowering plants have uncovered both common regulatory principles and unique players and/or regulatory interactions that underlie inflorescence architecture. Modulating activity of these regulators has already led to yield increases in the field. Additional insight into the underlying regulatory interactions and principles will not only uncover how their rewiring resulted in altered plant form, but will also enhance efforts at optimizing plant architecture in desirable ways in crop species.
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Affiliation(s)
- Yang Zhu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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13
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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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14
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Liu H, Liu H, Zhou L, Lin Z. Genetic Architecture of domestication- and improvement-related traits using a population derived from Sorghum virgatum and Sorghum bicolor. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:135-146. [PMID: 31128683 DOI: 10.1016/j.plantsci.2019.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/16/2019] [Accepted: 02/22/2019] [Indexed: 06/09/2023]
Abstract
The genetic basis of domestication and improvement remains largely unknown in sorghum as a typical multiple-origins species. In this study, the F2 and F3 populations derived from a cross between Sorghum virgatum and domesticated sorghum were used to study the genetic architecture of domestication- and improvement-related traits. We found that human selection had greatly reshaped sorghum through the Quantitative Trait Loci (QTLs) with large genetic effects in the traits of harvest, plant architecture and grain taste including the reduction of shattering, few branches, short plant stature and the removal of polyphenols from seed. The expansion of seed width was selected to improve the yield through accumulating small-effect QTLs. Two major QTLs of plant height (QTI-ph1 and dw1) were narrowed down into 24.5-kilobase (kb) and 13.9-kb, respectively. DNA diversity analysis and association mapping of dw1 gene suggested the functional variant (A1361 T) might originate from the same event not long time ago. Our results supported that parallel phenotypic changes across different species during domestication and improvement might share the same genetic basis, QTL × QTL interactions might not play an important role in the reshaping of traits during sorghum domestication and improvement, and offered new views on transgressive segregation and segregation distortion. Our study greatly deepens our understandings of the genetic basis of sorghum domestication and improvement.
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Affiliation(s)
- Huanhuan Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, Department of Plant Genomics and Bioinformatics, China Agricultural University, Beijing 100193, China
| | - Hangqin Liu
- National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, Department of Plant Genomics and Bioinformatics, China Agricultural University, Beijing 100193, China
| | - Leina Zhou
- National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, Department of Plant Genomics and Bioinformatics, China Agricultural University, Beijing 100193, China
| | - Zhongwei Lin
- National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, Department of Plant Genomics and Bioinformatics, China Agricultural University, Beijing 100193, China.
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15
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Yan S, Wang L, Zhao L, Wang H, Wang D. Evaluation of Genetic Variation among Sorghum Varieties from Southwest China via Genome Resequencing. THE PLANT GENOME 2018; 11:170098. [PMID: 30512039 DOI: 10.3835/plantgenome2017.11.0098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Little is known regarding genomic variation among glutinous sorghum [ (L.) Moench] varieties grown in southwest China, which are primarily used to brew the popular Jiang-flavor liquor. This study evaluated genomic variation among six representative sorghum accessions via whole-genome resequencing. The evaluation revealed 2365,363 single-nucleotide polymorphisms (SNPs), 394,365 insertions and deletions, and 47,567 copy number variations among the six genomes. Chromosomes 5 and 10 showed relatively high SNP densities, whereas whole-genome diversity in this population was low. In addition, some chromosomal loci exhibited obvious selection during the breeding process. Sorghum accessions from southwest China formed an elite germplasm population compared with the findings of other geographic populations, and the elite variety 'Hongyingzi' contained 79 unique genes primarily involved in basic metabolism. The six sorghum lines contained a large number of high-confidence genes, with Hongyingzi in particular possessing 104 unique genes. These findings advance our understanding of domestication of the sorghum genome, and Chinese sorghum accessions will be valuable resources for further research and breeding improvements.
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16
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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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17
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Clark LV, Dzyubenko E, Dzyubenko N, Bagmet L, Sabitov A, Chebukin P, Johnson DA, Kjeldsen JB, Petersen KK, Jørgensen U, Yoo JH, Heo K, Yu CY, Zhao H, Jin X, Peng J, Yamada T, Sacks EJ. Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia. ANNALS OF BOTANY 2016; 118:941-955. [PMID: 27451985 PMCID: PMC5055818 DOI: 10.1093/aob/mcw137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 05/24/2016] [Indexed: 05/08/2023]
Abstract
Background and aims Miscanthus is a genus of perennial C4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. ×giganteus, a hybrid between M. sinensis and M. sacchariflorus. Biomass yield and cold tolerance are of particular interest in Miscanthus, given that this crop is more temperate adapted than its C4 relatives maize, sorghum and sugarcane. Methods A plant exploration was conducted in eastern Russia, at the northern extreme of the native range for Miscanthus, with collections including 174 clonal germplasm accessions (160 M. sacchariflorus and 14 M. sinensis) from 47 sites. Accessions were genotyped by restriction site-associated DNA sequencing (RAD-seq) and plastid microsatellites. Key Results Miscanthus sinensis was found in maritime climates near Vladivostok (43·6°N) and on southern Sakhalin Island (46·6°N). Miscanthus sacchariflorus was found inland at latitudes as high as 49·3°N, where M. sinensis was absent. Most M. sacchariflorus accessions were diploid, but approx. 2 % were tetraploids. Molecular markers revealed little population structure (Jost's D < 0·007 among diploid groups) but high genetic diversity (expected heterozygosity = 0·14) within the collection of Russian M. sacchariflorus. Genome-wide association (GWA) analysis for traits measured at the collection sites revealed three M. sacchariflorus single nucleotide polymorphisms (SNPs) significantly associated with the number of stems per unit area, one with height and one with basal stem diameter; three were near or within previously described sorghum quantitative trait loci for related traits. Conclusions This new Miscanthus germplasm collection from eastern Russia will be useful for breeding Miscanthus and sugarcane cultivars with improved adaptation to cold. Moreover, a strategy is proposed to facilitate the rapid utilization of new germplasm collections: by implementing low-cost SNP genotyping to conduct GWA studies of phenotypic data obtained at collection sites, plant breeders can be provided with actionable information on which accessions have desirable traits and alleles.
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Affiliation(s)
- Lindsay V. Clark
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61802, USA
| | - Elena Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Nikolay Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Larisa Bagmet
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Andrey Sabitov
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Pavel Chebukin
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Douglas A. Johnson
- USDA-ARS Forage and Range Research Lab, Utah State University, Logan, UT 84322-6300, USA
| | | | - Karen Koefoed Petersen
- Department of Food Science, Aarhus University, Kirstinebjergvej 10, DK-5792 Årslev, Denmark
| | - Uffe Jørgensen
- Department of Agroecology, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark
| | - Ji Hye Yoo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Kweon Heo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Chang Yeon Yu
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Hua Zhao
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiaoli Jin
- Agronomy Department, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Junhua Peng
- Science and Technology Center, China Seed Group Co. Ltd, Wuhan, Hubei 430040, China
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Erik J. Sacks
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61802, USA
- *For correspondence. E-mail
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18
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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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Molecular Breeding of Sorghum bicolor, A Novel Energy Crop. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 321:221-57. [PMID: 26811289 DOI: 10.1016/bs.ircmb.2015.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Currently, molecular breeding is regarded as an important tool for the improvement of many crop species. However, in sorghum, recently heralded as an important bioenergy crop, progress in this field has been relatively slow and limited. In this review, we present existing efforts targeted at genetic characterization of sorghum mutants. We also comprehensively review the different attempts made toward the isolation of genes involved in agronomically important traits, including the dissection of some sorghum quantitative trait loci (QTLs). We also explore the current status of the use of transgenic techniques in sorghum, which should be crucial for advancing sorghum molecular breeding. Through this report, we provide a useful benchmark to help assess how much more sorghum genomics and molecular breeding could be improved.
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20
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Anami SE, Zhang L, Xia Y, Zhang Y, Liu Z, Jing H. Sweet sorghum ideotypes: genetic improvement of the biofuel syndrome. Food Energy Secur 2015. [DOI: 10.1002/fes3.63] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Sylvester Elikana Anami
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
- Institute of Biotechnology Research Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya
| | - Li‐Min Zhang
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Yan Xia
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Yu‐Miao Zhang
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Zhi‐Quan Liu
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Hai‐Chun Jing
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
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21
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Kong W, Kim C, Goff VH, Zhang D, Paterson AH. Genetic analysis of rhizomatousness and its relationship with vegetative branching of recombinant inbred lines of Sorghum bicolor × S. propinquum. AMERICAN JOURNAL OF BOTANY 2015; 102:718-24. [PMID: 26022486 DOI: 10.3732/ajb.1500035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/25/2015] [Indexed: 05/24/2023]
Abstract
PREMISE OF THE STUDY Rhizomes, subterranean stems that grow horizontally, are a storage organ that is highly associated with overwintering and regrowth. This quantitative study aimed to discover genetic determinants of rhizomatousness, an important trait related to perenniality and invasiveness. METHODS A population of 161 individuals of a recombinant inbred line (RIL) derived from morphologically distinct parents, Sorghum bicolor and Sorghum propinquum, which segregates for rhizomatousness, was phenotyped and genetically mapped. KEY RESULTS Seven genomic regions influenced rhizomatousness in this population; four were "consensus" regions that correspond with previously detected quantitative trait loci (QTLs) in an F2 population of the same pedigree and with different levels of vegetative branching. Because rhizomatousness is a plastic trait that is greatly influenced by environment, overlap between regions discovered in the RIL and F2 populations validates the position and effect of QTLs. Correspondence with regions influencing vegetative branching indicates that some genes and biochemical pathways may influence both vegetative branching and rhizomatousness, while genes influencing only one trait may confer divergent aspects of development of these organs. CONCLUSIONS Identifying genes conferring rhizomatousness and understanding their functions may provide opportunities to regulate plant growth for diverse applications. Increasing rhizomatousness may promote the productivity and perenniality of many grasses, especially biomass-dedicated crops, while decreasing rhizomatousness may improve monocarpic grain production and offer means to control many noxious weeds.
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Affiliation(s)
- Wenqian Kong
- Plant Genome Mapping Laboratory, 111 Riverbend Rd, University of Georgia, Athens, Georgia 30602 USA
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, 111 Riverbend Rd, University of Georgia, Athens, Georgia 30602 USA
| | - Valorie H Goff
- Plant Genome Mapping Laboratory, 111 Riverbend Rd, University of Georgia, Athens, Georgia 30602 USA
| | - Dong Zhang
- Plant Genome Mapping Laboratory, 111 Riverbend Rd, University of Georgia, Athens, Georgia 30602 USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, 111 Riverbend Rd, University of Georgia, Athens, Georgia 30602 USA
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