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Garin V, Diallo C, Tékété ML, Théra K, Guitton B, Dagno K, Diallo AG, Kouressy M, Leiser W, Rattunde F, Sissoko I, Touré A, Nébié B, Samaké M, Kholovà J, Berger A, Frouin J, Pot D, Vaksmann M, Weltzien E, Témé N, Rami JF. Characterization of adaptation mechanisms in sorghum using a multireference back-cross nested association mapping design and envirotyping. Genetics 2024; 226:iyae003. [PMID: 38381593 PMCID: PMC10990433 DOI: 10.1093/genetics/iyae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/20/2023] [Indexed: 02/23/2024] Open
Abstract
Identifying the genetic factors impacting the adaptation of crops to environmental conditions is of key interest for conservation and selection purposes. It can be achieved using population genomics, and evolutionary or quantitative genetics. Here we present a sorghum multireference back-cross nested association mapping population composed of 3,901 lines produced by crossing 24 diverse parents to 3 elite parents from West and Central Africa-back-cross nested association mapping. The population was phenotyped in environments characterized by differences in photoperiod, rainfall pattern, temperature levels, and soil fertility. To integrate the multiparental and multi-environmental dimension of our data we proposed a new approach for quantitative trait loci (QTL) detection and parental effect estimation. We extended our model to estimate QTL effect sensitivity to environmental covariates, which facilitated the integration of envirotyping data. Our models allowed spatial projections of the QTL effects in agro-ecologies of interest. We utilized this strategy to analyze the genetic architecture of flowering time and plant height, which represents key adaptation mechanisms in environments like West Africa. Our results allowed a better characterization of well-known genomic regions influencing flowering time concerning their response to photoperiod with Ma6 and Ma1 being photoperiod-sensitive and the region of possible candidate gene Elf3 being photoperiod-insensitive. We also accessed a better understanding of plant height genetic determinism with the combined effects of phenology-dependent (Ma6) and independent (qHT7.1 and Dw3) genomic regions. Therefore, we argue that the West and Central Africa-back-cross nested association mapping and the presented analytical approach constitute unique resources to better understand adaptation in sorghum with direct application to develop climate-smart varieties.
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Affiliation(s)
- Vincent Garin
- Crop Physiology Laboratory, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502 324, India
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Chiaka Diallo
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
- Département d’Enseignement et de Recherche des Sciences et Techniques Agricoles, Institut polytechnique rural de formation et de recherche appliquée de Katibougou, Koulikoro, BP 06, Mali
| | - Mohamed Lamine Tékété
- Institut d’Economie Rurale, Bamako, BP 262, Mali
- Faculté des Sciences et Techniques, Université des Sciences des Techniques et des Technologies de Bamako, Bamako, BP E 3206, Mali
| | | | - Baptiste Guitton
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Karim Dagno
- Institut d’Economie Rurale, Bamako, BP 262, Mali
| | | | | | - Willmar Leiser
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
| | - Fred Rattunde
- Agronomy Department, University of Wisconsin, Madison, WI 53705, WI, USA
| | - Ibrahima Sissoko
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
| | - Aboubacar Touré
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
| | - Baloua Nébié
- Dryland Crops Program, International Maize and Wheat Improvement Center (CIMMYT-Senegal) U/C CERAAS, Thiès, Po Box 3320, Senegal
| | - Moussa Samaké
- Faculté des Sciences et Techniques, Université des Sciences des Techniques et des Technologies de Bamako, Bamako, BP E 3206, Mali
| | - Jana Kholovà
- Crop Physiology Laboratory, International Crops Research Institute for the Semi-Arid Tropics, Patancheru, 502 324, India
- Department of Information Technologies, Faculty of Economics and Management, Czech University of Life Sciences, Prague, 165 00, Czech Republic
| | - Angélique Berger
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Julien Frouin
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - David Pot
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Michel Vaksmann
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
| | - Eva Weltzien
- Sorghum Program, International Crops Research Institute for the Semi-Arid Tropics, Bamako, BP 320, Mali
- Agronomy Department, University of Wisconsin, Madison, WI 53705, WI, USA
| | - Niaba Témé
- Institut d’Economie Rurale, Bamako, BP 262, Mali
| | - Jean-François Rami
- CIRAD, UMR AGAP Institut, Montpellier, F-34398, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, F-34398, France
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Yang L, Zhou Q, Sheng X, Chen X, Hua Y, Lin S, Luo Q, Yu B, Shao T, Wu Y, Chang J, Li Y, Tu M. Harnessing the Genetic Basis of Sorghum Biomass-Related Traits to Facilitate Bioenergy Applications. Int J Mol Sci 2023; 24:14549. [PMID: 37833996 PMCID: PMC10573072 DOI: 10.3390/ijms241914549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The extensive use of fossil fuels and global climate change have raised ever-increasing attention to sustainable development, global food security and the replacement of fossil fuels by renewable energy. Several C4 monocot grasses have excellent photosynthetic ability, stress tolerance and may rapidly produce biomass in marginal lands with low agronomic inputs, thus representing an important source of bioenergy. Among these grasses, Sorghum bicolor has been recognized as not only a promising bioenergy crop but also a research model due to its diploidy, simple genome, genetic diversity and clear orthologous relationship with other grass genomes, allowing sorghum research to be easily translated to other grasses. Although sorghum molecular genetic studies have lagged far behind those of major crops (e.g., rice and maize), recent advances have been made in a number of biomass-related traits to dissect the genetic loci and candidate genes, and to discover the functions of key genes. However, molecular and/or targeted breeding toward biomass-related traits in sorghum have not fully benefited from these pieces of genetic knowledge. Thus, to facilitate the breeding and bioenergy applications of sorghum, this perspective summarizes the bioenergy applications of different types of sorghum and outlines the genetic control of the biomass-related traits, ranging from flowering/maturity, plant height, internode morphological traits and metabolic compositions. In particular, we describe the dynamic changes of carbohydrate metabolism in sorghum internodes and highlight the molecular regulators involved in the different stages of internode carbohydrate metabolism, which affects the bioenergy utilization of sorghum biomass. We argue the way forward is to further enhance our understanding of the genetic mechanisms of these biomass-related traits with new technologies, which will lead to future directions toward tailored designing sorghum biomass traits suitable for different bioenergy applications.
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Affiliation(s)
- Lin Yang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Qin Zhou
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Xuan Sheng
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xiangqian Chen
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Yuqing Hua
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Shuang Lin
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Qiyun Luo
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Boju Yu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Ti Shao
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Yixiao Wu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Min Tu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
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Zhong S, Yang H, Chen C, Ren T, Li Z, Tan F, Luo P. Phenotypic characterization of the wheat temperature-sensitive leaf color mutant and physical mapping of mutant gene by reduced-representation sequencing. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111657. [PMID: 36813241 DOI: 10.1016/j.plantsci.2023.111657] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/10/2023] [Accepted: 02/18/2023] [Indexed: 06/18/2023]
Abstract
Few available leaf color mutants in crops have greatly limited the understanding of photosynthesis mechanisms, leading to few accomplishments in crop yield improvement via enhanced photosynthetic efficiency. Here, a noticeable albino mutant, CN19M06, was identified. A comparison between CN19M06 and the wild type CN19 at different temperatures showed that the albino mutant was temperature-sensitive and produced leaves with a decreased chlorophyll content at temperatures below 10 °C. Genetic analysis suggested that the albinism was controlled by one recessive nuclear gene named TSCA1, which was putatively assigned to the region of 718.1-729.8 Mb on chromosome 2AL using bulked-segregant analysis and double-digest restriction site-associated DNA. Finally, molecular linkage analysis physically anchored TSCA1 to a narrowed region of 718.8-725.3 Mb with a 6.5 Mb length on 2AL flanked by InDel 18 and InDel 25 with 0.7 cM genetic interval. Among the 111 annotated functional genes in the corresponding chromosomal region, only TraesCS2A01G487900 of the PAP fibrillin family was both related to chlorophyll metabolism and temperature sensitivity; therefore, it was considered the putative candidate gene of TSCA1. Overall, CN19M06 has great potential for exploring the molecular mechanism of photosynthesis and monitoring temperature changes in wheat production.
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Affiliation(s)
- Shengfu Zhong
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Huai Yang
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Chen Chen
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Tianheng Ren
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhi Li
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Feiquan Tan
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu 611130, China
| | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
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Li Y, Fang X, Lin Z. Convergent loss of anthocyanin pigments is controlled by the same MYB gene in cereals. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6089-6102. [PMID: 35724645 DOI: 10.1093/jxb/erac270] [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: 02/01/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Loss of anthocyanin pigments is a common transition during cereal domestication, diversification, and improvement. However, the genetic basis for this convergent transition in cereal remains largely unknown. Here, we identified a chromosomal syntenic block across different species that contained R2R3-MYB genes (c1/pl1) responsible for the convergent decoloring of anthocyanins in cereals. Quantitative trait locus (QTL) mapping identified a major QTL for aerial root color corresponding to pl1 and a major QTL for spikelet color corresponding to c1 on maize chromosomes 6 and 9, respectively. One insertion in the regulatory region that led to transcriptional down-regulation was present in maize pl1, and several insertions in the coding region resulting in loss of function occurred in maize c1. A transposable element insertion in the third exon of c1, leading to three new non-functional transcripts, was responsible for decoloring in foxtail millet. The c1/pl1 genes enhanced the transcription of the core enzyme-encoding genes, including pr1, fht1, a1, a2, bz1, and aat1 in the anthocyanin pathway, while they repressed the expression of fnsii1 in flavones, sm2 in maysin, and bx3, bx4, bx5, and bx10 in DIMBOA. Our results indicated that the convergent decoloring of these plants shared the same genetic basis across different cereal species.
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Affiliation(s)
- Yan Li
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China
| | - Xiaojian Fang
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China
| | - Zhongwei Lin
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, Hainan, China
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5
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Wu X, Liu Y, Luo H, Shang L, Leng C, Liu Z, Li Z, Lu X, Cai H, Hao H, Jing HC. Genomic footprints of sorghum domestication and breeding selection for multiple end uses. MOLECULAR PLANT 2022; 15:537-551. [PMID: 34999019 DOI: 10.1016/j.molp.2022.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 12/01/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Domestication and diversification have had profound effects on crop genomes. Originating in Africa and subsequently spreading to different continents, sorghum (Sorghum bicolor) has experienced multiple onsets of domestication and intensive breeding selection for various end uses. However, how these processes have shaped sorghum genomes is not fully understood. In the present study, population genomics analyses were performed on a worldwide collection of 445 sorghum accessions, covering wild sorghum and four end-use subpopulations with diverse agronomic traits. Frequent genetic exchanges were found among various subpopulations, and strong selective sweeps affected 14.68% (∼107.5 Mb) of the sorghum genome, including 3649, 4287, and 3888 genes during sorghum domestication, improvement of grain sorghum, and improvement of sweet sorghum, respectively. Eight different models of haplotype changes in domestication genes from wild sorghum to landraces and improved sorghum were observed, and Sh1- and SbTB1-type genes were representative of two prominent models, one of soft selection or multiple origins and one of hard selection or an early single domestication event. We also demonstrated that the Dry gene, which regulates stem juiciness, was unconsciously selected during the improvement of grain sorghum. Taken together, these findings provide new genomic insights into sorghum domestication and breeding selection, and will facilitate further dissection of the domestication and molecular breeding of sorghum.
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Affiliation(s)
- Xiaoyuan Wu
- 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
| | - Hong Luo
- 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
| | - Chuanyuan Leng
- 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
| | - Zhigang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaochun Lu
- Institute of Sorghum Research, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Hongwei Cai
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huaiqing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; 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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6
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NB-LRR-encoding genes conferring susceptibility to organophosphate pesticides in sorghum. Sci Rep 2021; 11:19828. [PMID: 34615901 PMCID: PMC8494876 DOI: 10.1038/s41598-021-98908-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022] Open
Abstract
Organophosphate is the commonly used pesticide to control pest outbreak, such as those by aphids in many crops. Despite its wide use, however, necrotic lesion and/or cell death following the application of organophosphate pesticides has been reported to occur in several species. To understand this phenomenon, called organophosphate pesticide sensitivity (OPS) in sorghum, we conducted QTL analysis in a recombinant inbred line derived from the Japanese cultivar NOG, which exhibits OPS. Mapping OPS in this population identified a prominent QTL on chromosome 5, which corresponded to Organophosphate-Sensitive Reaction (OSR) reported previously in other mapping populations. The OSR locus included a cluster of three genes potentially encoding nucleotide-binding leucine-rich repeat (NB-LRR, NLR) proteins, among which NLR-C was considered to be responsible for OPS in a dominant fashion. NLR-C was functional in NOG, whereas the other resistant parent, BTx623, had a null mutation caused by the deletion of promoter sequences. Our finding of OSR as a dominant trait is important not only in understanding the diversified role of NB-LRR proteins in cereals but also in securing sorghum breeding free from OPS.
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Belyaeva EV, Elkonin LA, Vladimirova AA, Panin VM. Manifestation of apomictic potentials in the line AS-3 of Sorghum bicolor (L.) Moench. PLANTA 2021; 254:37. [PMID: 34309737 DOI: 10.1007/s00425-021-03681-6] [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: 05/01/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
AS-3 line of Sorghum bicolor possesses functional components of apomixis-apospory, parthenogenesis and autonomous endospermogenesis. The data obtained indicate efficiency of selection for apomixis components in diploid species of cultivated crops. Apomixis (seed formation without fertilization) is one of most attractive phenomena in plant biology. In this paper, we provide the results of long-term selection for apomixis components in the progeny of grain sorghum (Sorghum bicolor (L.) Moench) hybrid plants with male sterility mutation. Selection was carried out for a high frequency of aposporous embryo sacs (ESs), autonomous pro-embryos, and the presence of maternal-type plants in test crosses with the line Volzhskoe-4v (V4v) homozygous for the Rs1 genes determining the red color of the leaves and stem of the hybrids. As a result of using this approach, the line, AS-3, was created, in which the frequency of ovaries with parthenogenetic embryos reached 42-45%. The autonomous development of embryos and endosperm was observed in the panicles of each of the 10 cytologically studied plants of this line. The frequency of parthenogenesis positively correlated with the high average daily air temperature during the first five out of 10 days preceding the onset of flowering (r = 0.75; P > 0.01). Genotyping of the plants from the progeny of hand-emasculated panicles of AS-3 pollinated with V4v performed using co-dominant SSR markers revealed that the F1 hybrids carrying the Rs1 gene (chromosome 6) possessed both paternal and maternal alleles of Sb1-10 (chromosome 4) and Xtxp320 (chromosome 10) markers, while in the maternal-type plants (rs1rs1), only the maternal alleles of these markers were present. In the endosperm of the kernels from which the maternal-type seedlings were obtained, only the maternal alleles were present, while in the endosperm of the kernels that produced hybrid seedlings, both the paternal and maternal alleles were observed. The data obtained indicate the presence of functional components of apomixis (apospory, parthenogenesis, autonomous endospermogenesis) in the grain sorghum line AS-3, and the efficiency of selection for apomixis in functionally diploid species of cultivated crops.
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Affiliation(s)
- Elena V Belyaeva
- Department of Biotechnology, Federal Center of Agriculture Research of the South-East Region, Saratov, 410010, Russia
| | - Lev A Elkonin
- Department of Biotechnology, Federal Center of Agriculture Research of the South-East Region, Saratov, 410010, Russia.
| | - Anastasia A Vladimirova
- Department of Biotechnology, Federal Center of Agriculture Research of the South-East Region, Saratov, 410010, Russia
| | - Valery M Panin
- Department of Biotechnology, Federal Center of Agriculture Research of the South-East Region, Saratov, 410010, Russia
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8
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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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9
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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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Nida H, Girma G, Mekonen M, Tirfessa A, Seyoum A, Bejiga T, Birhanu C, Dessalegn K, Senbetay T, Ayana G, Tesso T, Ejeta G, Mengiste T. Genome-wide association analysis reveals seed protein loci as determinants of variations in grain mold resistance in sorghum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1167-1184. [PMID: 33452894 DOI: 10.1007/s00122-020-03762-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
GWAS analysis revealed variations at loci harboring seed storage, late embryogenesis abundant protein, and a tannin biosynthesis gene associated with sorghum grain mold resistance. Grain mold is the most important disease of sorghum [Sorghum bicolor (L.) Moench]. It starts at the early stages of grain development due to concurrent infection by multiple fungal species. The genetic architecture of resistance to grain mold is poorly understood. Using a diverse set of 635 Ethiopian sorghum accessions, we conducted a multi-stage disease rating for resistance to grain mold under natural infestation in the field. Through genome-wide association analyses with 173,666 SNPs and multiple models, two novel loci were identified that were consistently associated with grain mold resistance across environments. Sequence variation at new loci containing sorghum KAFIRIN gene encoding a seed storage protein affecting seed texture and LATE EMBRYOGENESIS ABUNDANT 3 (LEA3) gene encoding a protein that accumulates in seeds, previously implicated in stress tolerance, were significantly associated with grain mold resistance. The KAFIRIN and LEA3 loci were also significant factors in grain mold resistance in accessions with non-pigmented grains. Moreover, we consistently detected the known SNP (S4_62316425) in TAN1 gene, a regulator of tannin accumulation in sorghum grain to be significantly associated with grain mold resistance. Identification of loci associated with new mechanisms of resistance provides fresh insight into genetic control of the trait, while the highly resistant accessions can serve as sources of resistance genes for breeding. Overall, our association data suggest the critical role of loci harboring seed protein genes and implicate grain chemical and physical properties in sorghum grain mold resistance.
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Affiliation(s)
- Habte Nida
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Gezahegn Girma
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Moges Mekonen
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Alemu Tirfessa
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Amare Seyoum
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Tamirat Bejiga
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Chemeda Birhanu
- Oromia Agricultural Research Institute, P.O. Box 81265, Addis Ababa, Ethiopia
| | - Kebede Dessalegn
- Oromia Agricultural Research Institute, P.O. Box 81265, Addis Ababa, Ethiopia
| | - Tsegau Senbetay
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Getachew Ayana
- Ethiopian Institute of Agricultural Research, P.O. Box 2003, Addis Ababa, Ethiopia
| | - Tesfaye Tesso
- Department of Agronomy, Kansas State University, 3007 Throckmorton PSC, 1712 Claflin Road, Manhattan, KS, 66506, USA
| | - Gebisa Ejeta
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
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Govindarajulu R, Hostetler AN, Xiao Y, Chaluvadi SR, Mauro-Herrera M, Siddoway ML, Whipple C, Bennetzen JL, Devos KM, Doust AN, Hawkins JS. Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum. G3-GENES GENOMES GENETICS 2021; 11:6128573. [PMID: 33712819 PMCID: PMC8022972 DOI: 10.1093/g3journal/jkab024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/12/2021] [Indexed: 12/13/2022]
Abstract
Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum and Sorghum bicolor inbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ∼1920 bin markers spanning ∼875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community.
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Affiliation(s)
| | - Ashley N Hostetler
- Department of Biology, West Virginia University, Morgantown, WV 26505, USA
| | - Yuguo Xiao
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | | | - Margarita Mauro-Herrera
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK 74078, USA
| | - Muriel L Siddoway
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Clinton Whipple
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | | | - Katrien M Devos
- Department of Crop and Soil Sciences (Institute for Plant Breeding, Genetics and Genomics), and Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Andrew N Doust
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK 74078, USA
| | - Jennifer S Hawkins
- Department of Biology, West Virginia University, Morgantown, WV 26505, USA
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12
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Sanjari S, Shobbar ZS, Ghanati F, Afshari-Behbahanizadeh S, Farajpour M, Jokar M, Khazaei A, Shahbazi M. Molecular, chemical, and physiological analyses of sorghum leaf wax under post-flowering drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 159:383-391. [PMID: 33450508 DOI: 10.1016/j.plaphy.2021.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/02/2021] [Indexed: 06/12/2023]
Abstract
Wax accumulation on the sorghum surface plays an important role in drought tolerance by preventing non-stomatal water loss. Thereby, the effect of post-flowering drought stress (PFDS) on the epicuticular wax (EW) amount, relative water content (RWC), chlorophyll, and grain yield in sorghum drought contrasting genotypes were investigated. The experiment was conducted as a split-plot based on randomized complete block design (RCBD) with two water treatments (normal watering and water holding after 50% flowering stage), and three genotypes (Kimia and KGS23 as drought-tolerant and Sepideh as drought-susceptible). Scanning electron microscopy and GC-MS analyses were used to determine the wax crystals density and its compositions, respectively. In addition, based on literature reviews and publicly available datasets, six wax biosynthesis drought stress-responsive genes were chosen for expression analysis. The results showed that the amounts of EW and wax crystals density were increased in Kimia and Sepideh genotypes and no changed in KGS23 genotype under drought stress. Chemical compositions of wax were classified into six major groups including alkanes, fatty acids, aldehydes, esters, alcohols, and cyclic compounds. Alkanes increment in drought-tolerant genotypes led to make an effective barrier against the drought stress to control water losses. In addition, the drought-tolerant genotypes had higher levels of RWC compared to the drought-susceptible ones, resulted in higher yield produced under drought condition. According to the results, SbWINL1, FATB, and CER1 genes play important roles in drought-induced wax biosynthesis. The results of the present study revealed a comprehensive view of the wax and its compositions and some involved genes in sorghum under drought stress.
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Affiliation(s)
- Sepideh Sanjari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Zahra-Sadat Shobbar
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Faezeh Ghanati
- Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | | | - Mostafa Farajpour
- Crop and Horticultural Science Research Department, Mazandaran Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Sari, Iran.
| | - Mojtaba Jokar
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Azim Khazaei
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Maryam Shahbazi
- Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran.
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Muturi PW, Mgonja M, Rubaihayo P, Mwololo JK. QTL Mapping of Traits Associated with Dual Resistance to the African Stem Borer ( Busseola fusca) and Spotted Stem Borer ( Chilo partellus) in Sorghum ( Sorghum bicolor). Int J Genomics 2021; 2021:7016712. [PMID: 33532486 PMCID: PMC7834829 DOI: 10.1155/2021/7016712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/14/2020] [Accepted: 11/16/2020] [Indexed: 11/21/2022] Open
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is an important food crop in semi-arid tropics. The crop grain yield ranges from 0.5 t/ha to 0.8 t/ha compared to potential yields of 10 t/ha. The African stem borer Busseola fusca Fuller (Noctuidae) and the spotted stem borer Chilo partellus Swinhoe (Crambidae), are among the most economically important insect pests of sorghum. The two borers can cause 15% - 80% grain yield loss in sorghum. Mapping of QTLs associated with resistance traits to the two stem borers is important towards marker-assisted breeding. The objective of this study was to map QTLs associated with resistance traits to B. fusca and C. partellus in sorghum. 243 F9:10 sorghum RILs derived from ICSV 745 (S) and PB 15520-1 (R) were selected for the study with 4,955 SNP markers. The RILs were evaluated in three sites. Data was collected on leaf feeding, deadheart, exit holes, stem tunnels, leaf toughness, seedling vigour, bloom waxiness, and leaf glossiness. ANOVA for all the traits was done using Genstat statistical software. Insect damage traits and morphological traits were correlated using Pearson's correlation coefficients. Genetic mapping was done using JoinMap 4 software, while QTL analysis was done using PLABQTL software. A likelihood odds ratio (LOD) score of 3.0 was used to declare linkage. Joint analyses across borer species and sites revealed 4 QTLs controlling deadheart formation; 6 controlling leaf feeding damage; 5 controlling exit holes and stem tunneling damages; 2 controlling bloom waxiness, leaf glossiness, and seedling vigour; 4 conditioning trichome density; and 6 conditioning leaf toughness. Joint analyses for B. fusca and C. partellus further revealed that marker CS132-2 colocalised for leaf toughness and stem tunneling traits on QTLs 1 and 2, respectively; thus, the two traits can be improved using the same linked marker. This study recommended further studies to identify gene(s) underlying the mapped QTLs.
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Affiliation(s)
- Phyllis W. Muturi
- Department of Agricultural Resource Management, University of Embu, P.O. Box 60100, Embu, Kenya
| | - Mary Mgonja
- Alliance for a Green Revolution in Africa, P.O. Box 34441, Dar es Salaam, Tanzania
| | - Patrick Rubaihayo
- Department of Agricultural Production, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - James K. Mwololo
- East and South African Research Program, International Crops Research Institute of the Semi-Arid Tropics (ICRISAT), P.O. Box 1096 Lilongwe, Malawi
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14
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Burgarella C, Berger A, Glémin S, David J, Terrier N, Deu M, Pot D. The Road to Sorghum Domestication: Evidence From Nucleotide Diversity and Gene Expression Patterns. FRONTIERS IN PLANT SCIENCE 2021; 12:666075. [PMID: 34527004 PMCID: PMC8435843 DOI: 10.3389/fpls.2021.666075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 07/20/2021] [Indexed: 05/17/2023]
Abstract
Native African cereals (sorghum, millets) ensure food security to millions of low-income people from low fertility and drought-prone regions of Africa and Asia. In spite of their agronomic importance, the genetic bases of their phenotype and adaptations are still not well-understood. Here we focus on Sorghum bicolor, which is the fifth cereal worldwide for grain production and constitutes the staple food for around 500 million people. We leverage transcriptomic resources to address the adaptive consequences of the domestication process. Gene expression and nucleotide variability were analyzed in 11 domesticated and nine wild accessions. We documented a downregulation of expression and a reduction of diversity both in nucleotide polymorphism (30%) and gene expression levels (18%) in domesticated sorghum. These findings at the genome-wide level support the occurrence of a global reduction of diversity during the domestication process, although several genes also showed patterns consistent with the action of selection. Nine hundred and forty-nine genes were significantly differentially expressed between wild and domesticated gene pools. Their functional annotation points to metabolic pathways most likely contributing to the sorghum domestication syndrome, such as photosynthesis and auxin metabolism. Coexpression network analyzes revealed 21 clusters of genes sharing similar expression patterns. Four clusters (totaling 2,449 genes) were significantly enriched in differentially expressed genes between the wild and domesticated pools and two were also enriched in domestication and improvement genes previously identified in sorghum. These findings reinforce the evidence that the combined and intricated effects of the domestication and improvement processes do not only affect the behaviors of a few genes but led to a large rewiring of the transcriptome. Overall, these analyzes pave the way toward the identification of key domestication genes valuable for genetic resources characterization and breeding purposes.
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Affiliation(s)
- Concetta Burgarella
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- *Correspondence: Concetta Burgarella
| | - Angélique Berger
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Sylvain Glémin
- CNRS, Univ. Rennes, ECOBIO – UMR 6553, Rennes, France
- Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jacques David
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Nancy Terrier
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Monique Deu
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP Institut, Montpellier, France
- AGAP Institut, Univ F-34398 Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- David Pot
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15
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Sapkota S, Boatwright JL, Jordan K, Boyles R, Kresovich S. Identification of Novel Genomic Associations and Gene Candidates for Grain Starch Content in Sorghum. Genes (Basel) 2020; 11:E1448. [PMID: 33276449 PMCID: PMC7760202 DOI: 10.3390/genes11121448] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/10/2020] [Accepted: 11/27/2020] [Indexed: 01/15/2023] Open
Abstract
Starch accumulated in the endosperm of cereal grains as reserve energy for germination serves as a staple in human and animal nutrition. Unraveling genetic control for starch metabolism is important for breeding grains with high starch content. In this study, we used a sorghum association panel with 389 individuals and 141,557 single nucleotide polymorphisms (SNPs) to fit linear mixed models (LMM) for identifying genomic regions and potential candidate genes associated with starch content. Three associated genomic regions, one in chromosome (chr) 1 and two novel associations in chr-8, were identified using combination of LMM and Bayesian sparse LMM. All significant SNPs were located within protein coding genes, with SNPs ∼ 52 Mb of chr-8 encoding a Casperian strip membrane protein (CASP)-like protein (Sobic.008G111500) and a heat shock protein (HSP) 90 (Sobic.008G111600) that were highly expressed in reproductive tissues including within the embryo and endosperm. The HSP90 is a potential hub gene with gene network of 75 high-confidence first interactors that is enriched for five biochemical pathways including protein processing. The first interactors of HSP90 also showed high transcript abundance in reproductive tissues. The candidates of this study are likely involved in intricate metabolic pathways and represent candidate gene targets for source-sink activities and drought and heat stress tolerance during grain filling.
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Affiliation(s)
- Sirjan Sapkota
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634, USA; (J.L.B.); (K.J.); (S.K.)
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
| | - J. Lucas Boatwright
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634, USA; (J.L.B.); (K.J.); (S.K.)
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
| | - Kathleen Jordan
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634, USA; (J.L.B.); (K.J.); (S.K.)
| | - Richard Boyles
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
- Pee Dee Research and Education Center, Clemson University, Florence, SC 29506, USA
| | - Stephen Kresovich
- Advanced Plant Technology Program, Clemson University, Clemson, SC 29634, USA; (J.L.B.); (K.J.); (S.K.)
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
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Species-Specific Duplication Event Associated with Elevated Levels of Nonstructural Carbohydrates in Sorghum bicolor. G3-GENES GENOMES GENETICS 2020; 10:1511-1520. [PMID: 32132167 PMCID: PMC7202026 DOI: 10.1534/g3.119.400921] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Simple sugars are the essential foundation to plant life, and thus, their production, utilization, and storage are highly regulated processes with many complex genetic controls. Despite their importance, many of the genetic and biochemical mechanisms remain unknown or uncharacterized. Sorghum, a highly productive, diverse C4 grass important for both industrial and subsistence agricultural systems, has considerable phenotypic diversity in the accumulation of nonstructural sugars in the stem. We use this crop species to examine the genetic controls of high levels of sugar accumulation, identify genetic mechanisms for the accumulation of nonstructural sugars, and link carbon allocation with iron transport. We identify a species-specific tandem duplication event controlling sugar accumulation using genome-wide association analysis, characterize multiple allelic variants causing increased sugar content, and provide further evidence of a putative neofunctionalization event conferring adaptability in Sorghum bicolor. Comparative genomics indicate that this event is unique to sorghum which may further elucidate evolutionary mechanisms for adaptation and divergence within the Poaceae. Furthermore, the identification and characterization of this event was only possible with the continued advancement and improvement of the reference genome. The characterization of this region and the process in which it was discovered serve as a reminder that any reference genome is imperfect and is in need of continual improvement.
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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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Mace E, Innes D, Hunt C, Wang X, Tao Y, Baxter J, Hassall M, Hathorn A, Jordan D. The Sorghum QTL Atlas: a powerful tool for trait dissection, comparative genomics and crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:751-766. [PMID: 30343386 DOI: 10.1007/s00122-018-3212-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/11/2018] [Indexed: 05/20/2023]
Abstract
We describe the development and application of the Sorghum QTL Atlas, a high-resolution, open-access research platform to facilitate candidate gene identification across three cereal species, sorghum, maize and rice. The mechanisms governing the genetic control of many quantitative traits are only poorly understood and have yet to be fully exploited. Over the last two decades, over a thousand QTL and GWAS studies have been published in the major cereal crops including sorghum, maize and rice. A large body of information has been generated on the genetic basis of quantitative traits, their genomic location, allelic effects and epistatic interactions. However, such QTL information has not been widely applied by cereal improvement programs and genetic researchers worldwide. In part this is due to the heterogeneous nature of QTL studies which leads QTL reliability variation from study to study. Using approaches to adjust the QTL confidence interval, this platform provides access to the most updated sorghum QTL information than any database available, spanning 23 years of research since 1995. The QTL database provides information on the predicted gene models underlying the QTL CI, across all sorghum genome assembly gene sets and maize and rice genome assemblies and also provides information on the diversity of the underlying genes and information on signatures of selection in sorghum. The resulting high-resolution, open-access research platform facilitates candidate gene identification across 3 cereal species, sorghum, maize and rice. Using a number of trait examples, we demonstrate the power and resolution of the resource to facilitate comparative genomics approaches to provide a bridge between genomics and applied breeding.
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Affiliation(s)
- Emma Mace
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia.
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia.
| | - David Innes
- Department of Agriculture and Fisheries, Ecosciences Precinct, Brisbane, QLD, 4102, Australia
| | - Colleen Hunt
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia
| | - Jared Baxter
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Michael Hassall
- Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, QLD, 4350, Australia
| | - Adrian Hathorn
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Warwick, QLD, 4370, Australia
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19
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Boyles RE, Brenton ZW, Kresovich S. Genetic and genomic resources of sorghum to connect genotype with phenotype in contrasting environments. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:19-39. [PMID: 30260043 DOI: 10.1111/tpj.14113] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 08/30/2018] [Accepted: 09/03/2018] [Indexed: 05/10/2023]
Abstract
With the recent development of genomic resources and high-throughput phenotyping platforms, the 21st century is primed for major breakthroughs in the discovery, understanding and utilization of plant genetic variation. Significant advances in agriculture remain at the forefront to increase crop production and quality to satisfy the global food demand in a changing climate all while reducing the environmental impacts of the world's food production. Sorghum, a resilient C4 grain and grass important for food and energy production, is being extensively dissected genetically and phenomically to help connect the relationship between genetic and phenotypic variation. Unlike genetically modified crops such as corn or soybean, sorghum improvement has relied heavily on public research; thus, many of the genetic resources serve a dual purpose for both academic and commercial pursuits. Genetic and genomic resources not only provide the foundation to identify and understand the genes underlying variation, but also serve as novel sources of genetic and phenotypic diversity in plant breeding programs. To better disseminate the collective information of this community, we discuss: (i) the genomic resources of sorghum that are at the disposal of the research community; (ii) the suite of sorghum traits as potential targets for increasing productivity in contrasting environments; and (iii) the prospective approaches and technologies that will help to dissect the genotype-phenotype relationship as well as those that will apply foundational knowledge for sorghum improvement.
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Affiliation(s)
- Richard E Boyles
- Pee Dee Research and Education Center, Clemson University, 2200 Pocket Rd, Florence, SC, 29506, USA
- Advanced Plant Technology Program, Clemson University, 105 Collings St, Clemson, SC, 29634, USA
| | - Zachary W Brenton
- Advanced Plant Technology Program, Clemson University, 105 Collings St, Clemson, SC, 29634, USA
- Department of Plant and Environment Sciences, Clemson University, 171 Poole Agricultural Center, Clemson, SC, 29634, USA
| | - Stephen Kresovich
- Advanced Plant Technology Program, Clemson University, 105 Collings St, Clemson, SC, 29634, USA
- Department of Plant and Environment Sciences, Clemson University, 171 Poole Agricultural Center, Clemson, SC, 29634, USA
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Ghosal S, Zheng B, Chapman SC, Potgieter AB, Jordan DR, Wang X, Singh AK, Singh A, Hirafuji M, Ninomiya S, Ganapathysubramanian B, Sarkar S, Guo W. A Weakly Supervised Deep Learning Framework for Sorghum Head Detection and Counting. PLANT PHENOMICS (WASHINGTON, D.C.) 2019; 2019:1525874. [PMID: 33313521 PMCID: PMC7706102 DOI: 10.34133/2019/1525874] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 05/30/2019] [Indexed: 05/19/2023]
Abstract
The yield of cereal crops such as sorghum (Sorghum bicolor L. Moench) depends on the distribution of crop-heads in varying branching arrangements. Therefore, counting the head number per unit area is critical for plant breeders to correlate with the genotypic variation in a specific breeding field. However, measuring such phenotypic traits manually is an extremely labor-intensive process and suffers from low efficiency and human errors. Moreover, the process is almost infeasible for large-scale breeding plantations or experiments. Machine learning-based approaches like deep convolutional neural network (CNN) based object detectors are promising tools for efficient object detection and counting. However, a significant limitation of such deep learning-based approaches is that they typically require a massive amount of hand-labeled images for training, which is still a tedious process. Here, we propose an active learning inspired weakly supervised deep learning framework for sorghum head detection and counting from UAV-based images. We demonstrate that it is possible to significantly reduce human labeling effort without compromising final model performance (R 2 between human count and machine count is 0.88) by using a semitrained CNN model (i.e., trained with limited labeled data) to perform synthetic annotation. In addition, we also visualize key features that the network learns. This improves trustworthiness by enabling users to better understand and trust the decisions that the trained deep learning model makes.
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Affiliation(s)
- Sambuddha Ghosal
- Department of Mechanical Engineering, Iowa State University, Ames, IA, USA
- Department of Computer Science, Iowa State University, Ames, IA, USA
| | - Bangyou Zheng
- CSIRO Agriculture and Food, St. Lucia, QLD, Australia
| | - Scott C. Chapman
- CSIRO Agriculture and Food, St. Lucia, QLD, Australia
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia
| | - Andries B. Potgieter
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Gatton, QLD, Australia
| | - David R. Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Warwick, QLD, Australia
| | - Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Warwick, QLD, Australia
| | | | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Masayuki Hirafuji
- International Field Phenomics Research Laboratory, Institute for Sustainable Agro-Ecosystem Services, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Seishi Ninomiya
- International Field Phenomics Research Laboratory, Institute for Sustainable Agro-Ecosystem Services, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, IA, USA
| | - Wei Guo
- International Field Phenomics Research Laboratory, Institute for Sustainable Agro-Ecosystem Services, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Girma G, Nida H, Seyoum A, Mekonen M, Nega A, Lule D, Dessalegn K, Bekele A, Gebreyohannes A, Adeyanju A, Tirfessa A, Ayana G, Taddese T, Mekbib F, Belete K, Tesso T, Ejeta G, Mengiste T. A Large-Scale Genome-Wide Association Analyses of Ethiopian Sorghum Landrace Collection Reveal Loci Associated With Important Traits. FRONTIERS IN PLANT SCIENCE 2019; 10:691. [PMID: 31191590 PMCID: PMC6549537 DOI: 10.3389/fpls.2019.00691] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 05/08/2019] [Indexed: 05/20/2023]
Abstract
The eastern Africa region, Ethiopia and its surroundings, is considered as the center of origin and diversity for sorghum, and has contributed to global sorghum genetic improvement. The germplasm from this region harbors enormous genetic variation for various traits but little is known regarding the genetic architecture of most traits. Here, 1425 Ethiopian landrace accessions were phenotyped under field conditions for presence or absence of awns, panicle compactness and shape, panicle exsertion, pericarp color, glume cover, plant height and smut resistance under diverse environmental conditions in Ethiopia. In addition, F1 hybrids obtained from a subset of 1341 accessions crossed to an A1 cytoplasmic male sterile line, ATx623, were scored for fertility/sterility reactions. Subsequently, genotyping-by-sequencing generated a total of 879,407 SNPs from which 72,190 robust SNP markers were selected after stringent quality control (QC). Pairwise distance-based hierarchical clustering identified 11 distinct groups. Of the genotypes assigned to either one of the 11 sub-populations, 65% had high ancestry membership coefficient with the likelihood of more than 0.60 and the remaining 35% represented highly admixed accessions. A genome-wide association study (GWAS) identified loci and SNPs associated with aforementioned traits. GWAS based on compressed mixed linear model (CMLM) identified SNPs with significant association (FDR ≤ 0.05) to the different traits studied. The percentage of total phenotypic variation explained with significant SNPs across traits ranged from 2 to 43%. Candidate genes showing significant association with different traits were identified. The sorghum bHLH transcription factor, ABORTED MICROSPORES was identified as a strong candidate gene conditioning male fertility. Notably, sorghum CLAVATA1 receptor like kinase, known for regulation of plant growth, and the ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR gene RAP2-7, known to suppress transition to flowering, were significantly associated with plant height. In addition, the YELLOW SEED1 like MYB transcription factor and TANNIN1 showed strong association with pericarp color validating previous observations. Overall, the genetic architecture of natural variation representing the complex Ethiopian sorghum germplasm was established. The study contributes to the characterization of genes and alleles controlling agronomic traits, and will serve as a source of markers for molecular breeding.
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Affiliation(s)
- Gezahegn Girma
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Habte Nida
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Amare Seyoum
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Moges Mekonen
- Chiro Agricultural Research Center, Ethiopian Institute of Agricultural Research, Chiro, Ethiopia
| | - Amare Nega
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Dagnachew Lule
- Bako Agricultural Research Center, Oromia Agricultural Research Institute, Bako, Ethiopia
| | - Kebede Dessalegn
- Bako Agricultural Research Center, Oromia Agricultural Research Institute, Bako, Ethiopia
| | - Alemnesh Bekele
- School of Plant Sciences, Haramaya University, Dire Dawa, Ethiopia
| | - Adane Gebreyohannes
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Adedayo Adeyanju
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Alemu Tirfessa
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Getachew Ayana
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Taye Taddese
- Malkassa Agricultural Research Center, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Firew Mekbib
- School of Plant Sciences, Haramaya University, Dire Dawa, Ethiopia
| | - Ketema Belete
- School of Plant Sciences, Haramaya University, Dire Dawa, Ethiopia
| | - Tesfaye Tesso
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - Gebisa Ejeta
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
- *Correspondence: Gebisa Ejeta,
| | - Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
- Tesfaye Mengiste,
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Harris-Shultz KR, Hayes CM, Knoll JE. Mapping QTLs and Identification of Genes Associated with Drought Resistance in Sorghum. Methods Mol Biol 2019; 1931:11-40. [PMID: 30652280 DOI: 10.1007/978-1-4939-9039-9_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Water limits global agricultural production. Increases in global aridity, a growing human population, and the depletion of aquifers will only increase the scarcity of water for agriculture. Water is essential for plant growth and in areas that are prone to drought, the use of drought-resistant crops is a long-term solution for growing more food for more people with less water. Sorghum is well adapted to hot and dry environments and has been used as a dietary staple for millions of people. Increasing the drought resistance in sorghum hybrids with no impact on yield is a continual objective for sorghum breeders. In this review, we describe the loci, quantitative trait loci (QTLs), or genes that have been identified for traits involved in drought avoidance (water-use efficiency, cuticular wax synthesis, trichome development and morphology, root system architecture) and drought tolerance (compatible solutes, pre- and post-flowering drought tolerance). Many of these identified genes and QTL regions have not been tested in hybrids and the effect of these genes, or their interactions, on yield must be understood in normal and drought-stressed conditions to understand the strength and weaknesses of their utility.
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Affiliation(s)
| | - Chad M Hayes
- Plant Stress and Germplasm Development Research, USDA-ARS, Lubbock, TX, USA
| | - Joseph E Knoll
- Crop Genetics and Breeding Research Unit, USDA-ARS, Tifton, GA, USA
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23
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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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Fujimoto M, Sazuka T, Oda Y, Kawahigashi H, Wu J, Takanashi H, Ohnishi T, Yoneda JI, Ishimori M, Kajiya-Kanegae H, Hibara KI, Ishizuna F, Ebine K, Ueda T, Tokunaga T, Iwata H, Matsumoto T, Kasuga S, Yonemaru JI, Tsutsumi N. Transcriptional switch for programmed cell death in pith parenchyma of sorghum stems. Proc Natl Acad Sci U S A 2018; 115:E8783-E8792. [PMID: 30150370 PMCID: PMC6140496 DOI: 10.1073/pnas.1807501115] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Pith parenchyma cells store water in various plant organs. These cells are especially important for producing sugar and ethanol from the sugar juice of grass stems. In many plants, the death of pith parenchyma cells reduces their stem water content. Previous studies proposed that a hypothetical D gene might be responsible for the death of stem pith parenchyma cells in Sorghum bicolor, a promising energy grass, although its identity and molecular function are unknown. Here, we identify the D gene and note that it is located on chromosome 6 in agreement with previous predictions. Sorghum varieties with a functional D allele had stems enriched with dry, dead pith parenchyma cells, whereas those with each of six independent nonfunctional D alleles had stems enriched with juicy, living pith parenchyma cells. D expression was spatiotemporally coupled with the appearance of dead, air-filled pith parenchyma cells in sorghum stems. Among D homologs that are present in flowering plants, Arabidopsis ANAC074 also is required for the death of stem pith parenchyma cells. D and ANAC074 encode previously uncharacterized NAC transcription factors and are sufficient to ectopically induce programmed death of Arabidopsis culture cells via the activation of autolytic enzymes. Taken together, these results indicate that D and its Arabidopsis ortholog, ANAC074, are master transcriptional switches that induce programmed death of stem pith parenchyma cells. Thus, targeting the D gene will provide an approach to breeding crops for sugar and ethanol production.
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Affiliation(s)
- Masaru Fujimoto
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Takashi Sazuka
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yoshihisa Oda
- Center for Frontier Research, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Hiroyuki Kawahigashi
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science, Tsukuba, Ibaraki 305-8602, Japan
| | - Jianzhong Wu
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science, Tsukuba, Ibaraki 305-8602, Japan
| | - Hideki Takanashi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Takayuki Ohnishi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Jun-Ichi Yoneda
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Motoyuki Ishimori
- Laboratory of Biometry and Bioinformatics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Hiromi Kajiya-Kanegae
- Laboratory of Biometry and Bioinformatics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Ken-Ichiro Hibara
- Laboratory of Plant Breeding and Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Fumiko Ishizuna
- Technology Advancement Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kazuo Ebine
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Takashi Ueda
- Division of Cellular Dynamics, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | | | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Takashi Matsumoto
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science, Tsukuba, Ibaraki 305-8602, Japan
| | - Shigemitsu Kasuga
- Faculty of Agriculture, Shinshu University, Minamiminowa, Nagano 399-4598, Japan
| | - Jun-Ichi Yonemaru
- National Agriculture and Food Research Organization (NARO), Institute of Crop Science, Tsukuba, Ibaraki 305-8602, Japan;
| | - Nobuhiro Tsutsumi
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan;
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Mathur S, Umakanth AV, Tonapi VA, Sharma R, Sharma MK. Sweet sorghum as biofuel feedstock: recent advances and available resources. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:146. [PMID: 28603553 PMCID: PMC5465577 DOI: 10.1186/s13068-017-0834-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 05/30/2017] [Indexed: 05/08/2023]
Abstract
Sweet sorghum is a promising target for biofuel production. It is a C4 crop with low input requirements and accumulates high levels of sugars in its stalks. However, large-scale planting on marginal lands would require improved varieties with optimized biofuel-related traits and tolerance to biotic and abiotic stresses. Considering this, many studies have been carried out to generate genetic and genomic resources for sweet sorghum. In this review, we discuss various attributes of sweet sorghum that make it an ideal candidate for biofuel feedstock, and provide an overview of genetic diversity, tools, and resources available for engineering and/or marker-assisting breeding of sweet sorghum. Finally, the progress made so far, in identification of genes/quantitative trait loci (QTLs) important for agronomic traits and ongoing molecular breeding efforts to generate improved varieties, has been discussed.
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Affiliation(s)
- Supriya Mathur
- Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - A. V. Umakanth
- Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - V. A. Tonapi
- Indian Council of Agricultural Research-Indian Institute of Millets Research, Hyderabad, India
| | - Rita Sharma
- Crop Genetics & Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Manoj K. Sharma
- Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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Boyles RE, Pfeiffer BK, Cooper EA, Rauh BL, Zielinski KJ, Myers MT, Brenton Z, Rooney WL, Kresovich S. Genetic dissection of sorghum grain quality traits using diverse and segregating populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:697-716. [PMID: 28028582 PMCID: PMC5360839 DOI: 10.1007/s00122-016-2844-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/17/2016] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Coordinated association and linkage mapping identified 25 grain quality QTLs in multiple environments, and fine mapping of the Wx locus supports the use of high-density genetic markers in linkage mapping. There is a wide range of end-use products made from cereal grains, and these products often demand different grain characteristics. Fortunately, cereal crop species including sorghum [Sorghum bicolor (L.) Moench] contain high phenotypic variation for traits influencing grain quality. Identifying genetic variants underlying this phenotypic variation allows plant breeders to develop genotypes with grain attributes optimized for their intended usage. Multiple sorghum mapping populations were rigorously phenotyped across two environments (SC Coastal Plain and Central TX) in 2 years for five major grain quality traits: amylose, starch, crude protein, crude fat, and gross energy. Coordinated association and linkage mapping revealed several robust QTLs that make prime targets to improve grain quality for food, feed, and fuel products. Although the amylose QTL interval spanned many megabases, the marker with greatest significance was located just 12 kb from waxy (Wx), the primary gene regulating amylose production in cereal grains. This suggests higher resolution mapping in recombinant inbred line (RIL) populations can be obtained when genotyped at a high marker density. The major QTL for crude fat content, identified in both a RIL population and grain sorghum diversity panel, encompassed the DGAT1 locus, a critical gene involved in maize lipid biosynthesis. Another QTL on chromosome 1 was consistently mapped in both RIL populations for multiple grain quality traits including starch, crude protein, and gross energy. Collectively, these genetic regions offer excellent opportunities to manipulate grain composition and set up future studies for gene validation.
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Affiliation(s)
- Richard E Boyles
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, 29634, USA.
- Advanced Plant Technology Program, Clemson University, Clemson, SC, 29634, USA.
| | - Brian K Pfeiffer
- Department of Soil and Crop Sciences, Texas A&M University, 2474 TAMU, College Station, TX, 77843, USA
| | - Elizabeth A Cooper
- Advanced Plant Technology Program, Clemson University, Clemson, SC, 29634, USA
| | - Bradley L Rauh
- Advanced Plant Technology Program, Clemson University, Clemson, SC, 29634, USA
| | - Kelsey J Zielinski
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, 28081, USA
| | - Matthew T Myers
- Advanced Plant Technology Program, Clemson University, Clemson, SC, 29634, USA
| | - Zachary Brenton
- Institute of Translational Genomics, Clemson University, Clemson, SC, 29634, USA
| | - William L Rooney
- Department of Soil and Crop Sciences, Texas A&M University, 2474 TAMU, College Station, TX, 77843, USA
| | - Stephen Kresovich
- Advanced Plant Technology Program, Clemson University, Clemson, SC, 29634, USA
- Institute of Translational Genomics, Clemson University, Clemson, SC, 29634, USA
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Rhodes D, Gadgil P, Perumal R, Tesso T, Herald TJ. Natural Variation and Genome-Wide Association Study of Antioxidants in a Diverse Sorghum Collection. Cereal Chem 2017. [DOI: 10.1094/cchem-03-16-0075-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Davina Rhodes
- USDA-ARS, Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, U.S.A. Names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and use of the name by the USDA implies no approval of the product to the exclusion of others that may also be suitable. USDA is an equal opportunity provider and employer
| | - Priyadarshini Gadgil
- USDA-ARS, Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, U.S.A. Names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and use of the name by the USDA implies no approval of the product to the exclusion of others that may also be suitable. USDA is an equal opportunity provider and employer
| | - Ramasamy Perumal
- Kansas State University, Agricultural Research Center, 1232 240th Ave., Hays, KS 67601, U.S.A
| | - Tesfaye Tesso
- Kansas State University, Department of Agronomy, Manhattan, KS 66506, U.S.A
| | - Thomas J. Herald
- USDA-ARS, Center for Grain and Animal Health Research, 1515 College Ave., Manhattan, KS 66502, U.S.A. Names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and use of the name by the USDA implies no approval of the product to the exclusion of others that may also be suitable. USDA is an equal opportunity provider and employer
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A Genomic Resource for the Development, Improvement, and Exploitation of Sorghum for Bioenergy. Genetics 2016; 204:21-33. [PMID: 27356613 PMCID: PMC5012387 DOI: 10.1534/genetics.115.183947] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 06/21/2016] [Indexed: 12/16/2022] Open
Abstract
With high productivity and stress tolerance, numerous grass genera of the Andropogoneae have emerged as candidates for bioenergy production. To optimize these candidates, research examining the genetic architecture of yield, carbon partitioning, and composition is required to advance breeding objectives. Significant progress has been made developing genetic and genomic resources for Andropogoneae, and advances in comparative and computational genomics have enabled research examining the genetic basis of photosynthesis, carbon partitioning, composition, and sink strength. To provide a pivotal resource aimed at developing a comparative understanding of key bioenergy traits in the Andropogoneae, we have established and characterized an association panel of 390 racially, geographically, and phenotypically diverse Sorghum bicolor accessions with 232,303 genetic markers. Sorghum bicolor was selected because of its genomic simplicity, phenotypic diversity, significant genomic tools, and its agricultural productivity and resilience. We have demonstrated the value of sorghum as a functional model for candidate gene discovery for bioenergy Andropogoneae by performing genome-wide association analysis for two contrasting phenotypes representing key components of structural and non-structural carbohydrates. We identified potential genes, including a cellulase enzyme and a vacuolar transporter, associated with increased non-structural carbohydrates that could lead to bioenergy sorghum improvement. Although our analysis identified genes with potentially clear functions, other candidates did not have assigned functions, suggesting novel molecular mechanisms for carbon partitioning traits. These results, combined with our characterization of phenotypic and genetic diversity and the public accessibility of each accession and genomic data, demonstrate the value of this resource and provide a foundation for future improvement of sorghum and related grasses for bioenergy production.
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The Sorghum Gene for Leaf Color Changes upon Wounding (P) Encodes a Flavanone 4-Reductase in the 3-Deoxyanthocyanidin Biosynthesis Pathway. G3-GENES GENOMES GENETICS 2016; 6:1439-47. [PMID: 26994288 PMCID: PMC4856094 DOI: 10.1534/g3.115.026104] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Upon wounding or pathogen invasion, leaves of sorghum [Sorghum bicolor (L.) Moench] plants with the P gene turn purple, whereas leaves with the recessive allele turn brown or tan. This purple phenotype is determined by the production of two 3-deoxyanthocyanidins, apigeninidin and luteolinidin, which are not produced by the tan-phenotype plants. Using map-based cloning in progeny from a cross between purple Nakei-MS3B (PP) and tan Greenleaf (pp) cultivars, we isolated this gene, which was located in a 27-kb genomic region around the 58.1 Mb position on chromosome 6. Four candidate genes identified in this region were similar to the maize leucoanthocyanidin reductase gene. None of them was expressed before wounding, and only the Sb06g029550 gene was induced in both cultivars after wounding. The Sb06g029550 protein was detected in Nakei-MS3B, but only slightly in Greenleaf, in which it may be unstable because of a Cys252Tyr substitution. A recombinant Sb06g029550 protein had a specific flavanone 4-reductase activity, and converted flavanones (naringenin or eriodictyol) to flavan-4-ols (apiforol or luteoforol) in vitro. Our data indicate that the Sb06g029550 gene is involved in the 3-deoxyanthocyanidin synthesis pathway.
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Gelli M, Mitchell SE, Liu K, Clemente TE, Weeks DP, Zhang C, Holding DR, Dweikat IM. Mapping QTLs and association of differentially expressed gene transcripts for multiple agronomic traits under different nitrogen levels in sorghum. BMC PLANT BIOLOGY 2016; 16:16. [PMID: 26759170 PMCID: PMC4710988 DOI: 10.1186/s12870-015-0696-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/21/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND Sorghum is an important C4 crop which relies on applied Nitrogen fertilizers (N) for optimal yields, of which substantial amounts are lost into the atmosphere. Understanding the genetic variation of sorghum in response to limited nitrogen supply is important for elucidating the underlying genetic mechanisms of nitrogen utilization. RESULTS A bi-parental mapping population consisting of 131 recombinant inbred lines (RILs) was used to map quantitative trait loci (QTLs) influencing different agronomic traits evaluated under normal N (100 kg.ha(-1) fertilizer) and low N (0 kg.ha(-1) fertilizer) conditions. A linkage map spanning 1614 cM was developed using 642 polymorphic single nucleotide polymorphisms (SNPs) detected in the population using Genotyping-By-Sequencing (GBS) technology. Composite interval mapping detected a total of 38 QTLs for 11 agronomic traits tested under different nitrogen levels. The phenotypic variation explained by individual QTL ranged from 6.2 to 50.8%. Illumina RNA sequencing data generated on seedling root tissues revealed 726 differentially expressed gene (DEG) transcripts between parents, of which 108 were mapped close to the QTL regions. CONCLUSIONS Co-localized regions affecting multiple traits were detected on chromosomes 1, 5, 6, 7 and 9. These potentially pleiotropic regions were coincident with the genomic regions of cloned QTLs, including genes associated with flowering time, Ma3 on chromosome 1 and Ma1 on chromosome 6, gene associated with plant height, Dw2 on chromosome 6. In these regions, RNA sequencing data showed differential expression of transcripts related to nitrogen metabolism (Ferredoxin-nitrate reductase), glycolysis (Phosphofructo-2-kinase), seed storage proteins, plant hormone metabolism and membrane transport. The differentially expressed transcripts underlying the pleiotropic QTL regions could be potential targets for improving sorghum performance under limited N fertilizer through marker assisted selection.
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Affiliation(s)
- Malleswari Gelli
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
| | - Sharon E Mitchell
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA.
- Institute of Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
| | - Kan Liu
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA.
- Institute of Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
| | - Thomas E Clemente
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
| | - Donald P Weeks
- Department of Biochemistry, University of Nebraska, Lincoln, NE, 68588, USA.
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588, USA.
- Institute of Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA.
| | - David R Holding
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
| | - Ismail M Dweikat
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
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Mizuno H, Kasuga S, Kawahigashi H. The sorghum SWEET gene family: stem sucrose accumulation as revealed through transcriptome profiling. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:127. [PMID: 27330561 PMCID: PMC4912755 DOI: 10.1186/s13068-016-0546-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/03/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND SWEET is a newly identified family of sugar transporters. Although SWEET transporters have been characterized by using Arabidopsis and rice, very little knowledge of sucrose accumulation in the stem region is available, as these model plants accumulate little sucrose in their stems. To elucidate the expression of key SWEET genes involved in sucrose accumulation of sorghum, we performed transcriptome profiling by RNA-seq, categorization using phylogenetic trees, analysis of chromosomal synteny, and comparison of amino acid sequences between SIL-05 (a sweet sorghum) and BTx623 (a grain sorghum). RESULTS We identified 23 SWEET genes in the sorghum genome. In the leaf, SbSWEET8-1 was highly expressed and was grouped in the same clade as AtSWEET11 and AtSWEET12 that play a role in the efflux of photosynthesized sucrose. The key genes in sucrose synthesis (SPS3) and that in another step of sugar transport (SbSUT1 and SbSUT2) were also highly expressed, suggesting that sucrose is newly synthesized and actively exported from the leaf. In the stem, SbSWEET4-3 was uniquely highly expressed. SbSWEET4-1, SbSWEET4-2, and SbSWEET4-3 were categorized into the same clade, but their tissue specificities were different, suggesting that SbSWEET4-3 is a sugar transporter with specific roles in the stem. We found a putative SWEET4-3 ortholog in the corresponding region of the maize chromosome, but not the rice chromosome, suggesting that SbSWEET4-3 was copied after the branching of sorghum and maize from rice. In the panicle from the heading through to 36 days afterward, SbSWEET2-1 and SbSWEET7-1 were expressed and grouped in the same clade as rice OsSWEET11/Xa13 that is essential for seed development. SbSWEET9-3 was highly expressed in the panicle only just after heading and was grouped into the same clade as AtSWEET8/RPG1 that is essential for pollen viability. Five of 23 SWEET genes had SNPs that caused nonsynonymous amino acid substitutions between SIL-05 and BTx623. CONCLUSIONS We determined the key SWEET genes for technological improvement of sorghum in the production of biofuels: SbSWEET8-1 for efflux of sucrose from the leaf; SbSWEET4-3 for unloading sucrose from the phloem in the stem; SbSWEET2-1 and SbSWEET7-1 for seed development; SbSWEET9-3 for pollen nutrition.
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Affiliation(s)
- Hiroshi Mizuno
- />Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602 Japan
- />Institute of Crop Science (NICS), National Agriculture and Food Research Organization, 1-2, Owashi, Tsukuba, Ibaraki 305-8602 Japan
| | - Shigemitsu Kasuga
- />Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Nagano, 399-4598 Japan
| | - Hiroyuki Kawahigashi
- />Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602 Japan
- />Institute of Crop Science (NICS), National Agriculture and Food Research Organization, 1-2, Owashi, Tsukuba, Ibaraki 305-8602 Japan
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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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Wang X, Mace E, Hunt C, Cruickshank A, Henzell R, Parkes H, Jordan D. Two distinct classes of QTL determine rust resistance in sorghum. BMC PLANT BIOLOGY 2014; 14:366. [PMID: 25551674 PMCID: PMC4335369 DOI: 10.1186/s12870-014-0366-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 12/05/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND Agriculture is facing enormous challenges to feed a growing population in the face of rapidly evolving pests and pathogens. The rusts, in particular, are a major pathogen of cereal crops with the potential to cause large reductions in yield. Improving stable disease resistance is an on-going major and challenging focus for many plant breeding programs, due to the rapidly evolving nature of the pathogen. Sorghum is a major summer cereal crop that is also a host for a rust pathogen Puccinia purpurea, which occurs in almost all sorghum growing areas of the world, causing direct and indirect yield losses in sorghum worldwide, however knowledge about its genetic control is still limited. In order to further investigate this issue, QTL and association mapping methods were implemented to study rust resistance in three bi-parental populations and an association mapping set of elite breeding lines in different environments. RESULTS In total, 64 significant or highly significant QTL and 21 suggestive rust resistance QTL were identified representing 55 unique genomic regions. Comparisons across populations within the current study and with rust QTL identified previously in both sorghum and maize revealed a high degree of correspondence in QTL location. Negative phenotypic correlations were observed between rust, maturity and height, indicating a trend for both early maturing and shorter genotypes to be more susceptible to rust. CONCLUSIONS The significant amount of QTL co-location across traits, in addition to the consistency in the direction of QTL allele effects, has provided evidence to support pleiotropic QTL action across rust, height, maturity and stay-green, supporting the role of carbon stress in susceptibility to rust. Classical rust resistance QTL regions that did not co-locate with height, maturity or stay-green QTL were found to be significantly enriched for the defence-related NBS-encoding gene family, in contrast to the lack of defence-related gene enrichment in multi-trait effect rust resistance QTL. The distinction of disease resistance QTL hot-spots, enriched with defence-related gene families from QTL which impact on development and partitioning, provides plant breeders with knowledge which will allow for fast-tracking varieties with both durable pathogen resistance and appropriate adaptive traits.
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Affiliation(s)
- Xuemin Wang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, Australia.
| | - Emma Mace
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | - Colleen Hunt
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, Australia.
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | - Alan Cruickshank
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | - Robert Henzell
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | - Heidi Parkes
- Department of Agriculture, Fisheries & Forestry (DAFF), Stanthorpe, QLD, Australia.
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, Australia.
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Rhodes DH, Hoffmann L, Rooney WL, Ramu P, Morris GP, Kresovich S. Genome-wide association study of grain polyphenol concentrations in global sorghum [Sorghum bicolor (L.) Moench] germplasm. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:10916-27. [PMID: 25272193 DOI: 10.1021/jf503651t] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Identifying natural variation of health-promoting compounds in staple crops and characterizing its genetic basis can help improve human nutrition through crop biofortification. Some varieties of sorghum, a staple cereal crop grown worldwide, have high concentrations of proanthocyanidins and 3-deoxyanthocyanidins, polyphenols with antioxidant and anti-inflammatory properties. We quantified total phenols, proanthocyanidins, and 3-deoxyanthocyanidins in a global sorghum diversity panel (n = 381) using near-infrared spectroscopy (NIRS), and characterized the patterns of variation with respect to geographic origin and botanical race. A genome-wide association study (GWAS) with 404,628 SNP markers identified novel quantitative trait loci for sorghum polyphenols, some of which colocalized with homologues of flavonoid pathway genes from other plants, including an orthologue of maize (Zea mays) Pr1 and a homologue of Arabidopsis (Arabidopsis thaliana) TT16. This survey of grain polyphenol variation in sorghum germplasm and catalog of flavonoid pathway loci may be useful to guide future enhancement of cereal polyphenols.
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Affiliation(s)
- Davina H Rhodes
- Department of Biological Sciences, University of South Carolina , Columbia, South Carolina 29208, United States
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Mace E, Tai S, Innes D, Godwin I, Hu W, Campbell B, Gilding E, Cruickshank A, Prentis P, Wang J, Jordan D. The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes. BMC PLANT BIOLOGY 2014; 14:253. [PMID: 25928459 PMCID: PMC4189741 DOI: 10.1186/s12870-014-0253-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 09/20/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Increased disease resistance is a key target of cereal breeding programs, with disease outbreaks continuing to threaten global food production, particularly in Africa. Of the disease resistance gene families, the nucleotide-binding site plus leucine-rich repeat (NBS-LRR) family is the most prevalent and ancient and is also one of the largest gene families known in plants. The sequence diversity in NBS-encoding genes was explored in sorghum, a critical food staple in Africa, with comparisons to rice and maize and with comparisons to fungal pathogen resistance QTL. RESULTS In sorghum, NBS-encoding genes had significantly higher diversity in comparison to non NBS-encoding genes and were significantly enriched in regions of the genome under purifying and balancing selection, both through domestication and improvement. Ancestral genes, pre-dating species divergence, were more abundant in regions with signatures of selection than in regions not under selection. Sorghum NBS-encoding genes were also significantly enriched in the regions of the genome containing fungal pathogen disease resistance QTL; with the diversity of the NBS-encoding genes influenced by the type of co-locating biotic stress resistance QTL. CONCLUSIONS NBS-encoding genes are under strong selection pressure in sorghum, through the contrasting evolutionary processes of purifying and balancing selection. Such contrasting evolutionary processes have impacted ancestral genes more than species-specific genes. Fungal disease resistance hot-spots in the genome, with resistance against multiple pathogens, provides further insight into the mechanisms that cereals use in the "arms race" with rapidly evolving pathogens in addition to providing plant breeders with selection targets for fast-tracking the development of high performing varieties with more durable pathogen resistance.
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Affiliation(s)
- Emma Mace
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | | | - David Innes
- DAFFQ, Cooper's Plains, Brisbane, QLD, Australia.
| | - Ian Godwin
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, QLD, Australia.
| | | | | | - Edward Gilding
- The Institute of Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
| | - Alan Cruickshank
- Department of Agriculture, Fisheries & Forestry (DAFF), Warwick, QLD, Australia.
| | - Peter Prentis
- Queensland University of Technology, Brisbane, QLD, Australia.
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China.
- Department of Biology, University of Copenhagen, DK-2200, Copenhagen, Denmark.
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, DK-2200, Copenhagen, Denmark.
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, QLD, Australia.
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Mace ES, Tai S, Gilding EK, Li Y, Prentis PJ, Bian L, Campbell BC, Hu W, Innes DJ, Han X, Cruickshank A, Dai C, Frère C, Zhang H, Hunt CH, Wang X, Shatte T, Wang M, Su Z, Li J, Lin X, Godwin ID, Jordan DR, Wang J. Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum. Nat Commun 2014; 4:2320. [PMID: 23982223 PMCID: PMC3759062 DOI: 10.1038/ncomms3320] [Citation(s) in RCA: 260] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 07/17/2013] [Indexed: 11/09/2022] Open
Abstract
Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world’s poorest people. Its small diploid genome and phenotypic diversity make it an ideal C4 grass model as a complement to C3 rice. Here we present high coverage (16–45 × ) resequenced genomes of 44 sorghum lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group. We also report the first resequenced genome of S. propinquum, identifying 8 M high-quality SNPs, 1.9 M indels and specific gene loss and gain events in S. bicolor. We observe strong racial structure and a complex domestication history involving at least two distinct domestication events. These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum, providing an unmatched resource for the genetic improvement of sorghum and other grass species. Sorghum is a drought-resistant food and feed cereal crop used by over half a billion of the world’s poorest people. Here the authors present high-coverage resequencing genome data of 44 sorghum lines of varying geographic and taxonomic origin, which include a number of sorghum wild relatives.
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Affiliation(s)
- Emma S Mace
- 1] Department of Agriculture, Fisheries and Forestry Queensland (DAFFQ), Warwick, Queensland 4370, Australia [2]
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Evans J, McCormick RF, Morishige D, Olson SN, Weers B, Hilley J, Klein P, Rooney W, Mullet J. Extensive variation in the density and distribution of DNA polymorphism in sorghum genomes. PLoS One 2013; 8:e79192. [PMID: 24265758 PMCID: PMC3827139 DOI: 10.1371/journal.pone.0079192] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 09/24/2013] [Indexed: 11/25/2022] Open
Abstract
Sorghum genotypes currently used for grain production in the United States were developed from African landraces that were imported starting in the mid-to-late 19th century. Farmers and plant breeders selected genotypes for grain production with reduced plant height, early flowering, increased grain yield, adaptation to drought, and improved resistance to lodging, diseases and pests. DNA polymorphisms that distinguish three historically important grain sorghum genotypes, BTx623, BTx642 and Tx7000, were characterized by genome sequencing, genotyping by sequencing, genetic mapping, and pedigree-based haplotype analysis. The distribution and density of DNA polymorphisms in the sequenced genomes varied widely, in part because the lines were derived through breeding and selection from diverse Kafir, Durra, and Caudatum race accessions. Genomic DNA spanning dw1 (SBI-09) and dw3 (SBI-07) had identical haplotypes due to selection for reduced height. Lower SNP density in genes located in pericentromeric regions compared with genes located in euchromatic regions is consistent with background selection in these regions of low recombination. SNP density was higher in euchromatic DNA and varied >100-fold in contiguous intervals that spanned up to 300 Kbp. The localized variation in DNA polymorphism density occurred throughout euchromatic regions where recombination is elevated, however, polymorphism density was not correlated with gene density or DNA methylation. Overall, sorghum chromosomes contain distal euchromatic regions characterized by extensive, localized variation in DNA polymorphism density, and large pericentromeric regions of low gene density, diversity, and recombination.
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Affiliation(s)
- Joseph Evans
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Ryan F. McCormick
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Daryl Morishige
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Sara N. Olson
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Brock Weers
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Josie Hilley
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Patricia Klein
- Department of Horticulture, Texas A&M University, College Station, Texas, United States of America
| | - William Rooney
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
| | - John Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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Dissecting genome-wide association signals for loss-of-function phenotypes in sorghum flavonoid pigmentation traits. G3-GENES GENOMES GENETICS 2013; 3:2085-94. [PMID: 24048646 PMCID: PMC3815067 DOI: 10.1534/g3.113.008417] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genome-wide association studies are a powerful method to dissect the genetic basis of traits, although in practice the effects of complex genetic architecture and population structure remain poorly understood. To compare mapping strategies we dissected the genetic control of flavonoid pigmentation traits in the cereal grass sorghum by using high-resolution genotyping-by-sequencing single-nucleotide polymorphism markers. Studying the grain tannin trait, we find that general linear models (GLMs) are not able to precisely map tan1-a, a known loss-of-function allele of the Tannin1 gene, with either a small panel (n = 142) or large association panel (n = 336), and that indirect associations limit the mapping of the Tannin1 locus to Mb-resolution. A GLM that accounts for population structure (Q) or standard mixed linear model that accounts for kinship (K) can identify tan1-a, whereas a compressed mixed linear model performs worse than the naive GLM. Interestingly, a simple loss-of-function genome scan, for genotype-phenotype covariation only in the putative loss-of-function allele, is able to precisely identify the Tannin1 gene without considering relatedness. We also find that the tan1-a allele can be mapped with gene resolution in a biparental recombinant inbred line family (n = 263) using genotyping-by-sequencing markers but lower precision in the mapping of vegetative pigmentation traits suggest that consistent gene-level resolution will likely require larger families or multiple recombinant inbred lines. These findings highlight that complex association signals can emerge from even the simplest traits given epistasis and structured alleles, but that gene-resolution mapping of these traits is possible with high marker density and appropriate models.
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Fernández L, de Haro LA, Distefano AJ, Carolina Martínez M, Lía V, Papa JC, Olea I, Tosto D, Esteban Hopp H. Population genetics structure of glyphosate-resistant Johnsongrass (Sorghum halepense L. Pers) does not support a single origin of the resistance. Ecol Evol 2013; 3:3388-400. [PMID: 24223277 PMCID: PMC3797486 DOI: 10.1002/ece3.671] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 06/09/2013] [Accepted: 06/10/2013] [Indexed: 11/11/2022] Open
Abstract
Single sequence repeats (SSR) developed for Sorghum bicolor were used to characterize the genetic distance of 46 different Sorghum halepense (Johnsongrass) accessions from Argentina some of which have evolved toward glyphosate resistance. Since Johnsongrass is an allotetraploid and only one subgenome is homologous to cultivated sorghum, some SSR loci amplified up to two alleles while others (presumably more conserved loci) amplified up to four alleles. Twelve SSR providing information of 24 loci representative of Johnsongrass genome were selected for genetic distance characterization. All of them were highly polymorphic, which was evidenced by the number of different alleles found in the samples studied, in some of them up to 20. UPGMA and Mantel analysis showed that Johnsongrass glyphosate-resistant accessions that belong to different geographic regions do not share similar genetic backgrounds. In contrast, they show closer similarity to their neighboring susceptible counterparts. Discriminant Analysis of Principal Components using the clusters identified by K-means support the lack of a clear pattern of association among samples and resistance status or province of origin. Consequently, these results do not support a single genetic origin of glyphosate resistance. Nucleotide sequencing of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) encoding gene from glyphosate-resistant and susceptible accessions collected from different geographic origins showed that none presented expected mutations in aminoacid positions 101 and 106 which are diagnostic of target-site resistance mechanism.
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Affiliation(s)
- Luis Fernández
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA Castelar) N. Repetto y Los Reseros, 1686, Hurlingham, Argentina
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Thurber CS, Ma JM, Higgins RH, Brown PJ. Retrospective genomic analysis of sorghum adaptation to temperate-zone grain production. Genome Biol 2013; 14:R68. [PMID: 23803286 PMCID: PMC3706989 DOI: 10.1186/gb-2013-14-6-r68] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/11/2013] [Accepted: 06/26/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sorghum is a tropical C4 cereal that recently adapted to temperate latitudes and mechanized grain harvest through selection for dwarfism and photoperiod-insensitivity. Quantitative trait loci for these traits have been introgressed from a dwarf temperate donor into hundreds of diverse sorghum landraces to yield the Sorghum Conversion lines. Here, we report the first comprehensive genomic analysis of the molecular changes underlying this adaptation. RESULTS We apply genotyping-by-sequencing to 1,160 Sorghum Conversion lines and their exotic progenitors, and map donor introgressions in each Sorghum Conversion line. Many Sorghum Conversion lines carry unexpected haplotypes not found in either presumed parent. Genome-wide mapping of introgression frequencies reveals three genomic regions necessary for temperate adaptation across all Sorghum Conversion lines, containing the Dw1, Dw2, and Dw3 loci on chromosomes 9, 6, and 7 respectively. Association mapping of plant height and flowering time in Sorghum Conversion lines detects significant associations in the Dw1 but not the Dw2 or Dw3 regions. Subpopulation-specific introgression mapping suggests that chromosome 6 contains at least four loci required for temperate adaptation in different sorghum genetic backgrounds. The Dw1 region fractionates into separate quantitative trait loci for plant height and flowering time. CONCLUSIONS Generating Sorghum Conversion lines has been accompanied by substantial unintended gene flow. Sorghum adaptation to temperate-zone grain production involves a small number of genomic regions, each containing multiple linked loci for plant height and flowering time. Further characterization of these loci will accelerate the adaptation of sorghum and related grasses to new production systems for food and fuel.
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Affiliation(s)
- Carrie S Thurber
- Energy Biosciences Institute, University of Illinois, Urbana, IL, USA
| | - Justin M Ma
- Energy Biosciences Institute, University of Illinois, Urbana, IL, USA
| | - Race H Higgins
- Energy Biosciences Institute, University of Illinois, Urbana, IL, USA
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Patrick J Brown
- Energy Biosciences Institute, University of Illinois, Urbana, IL, USA
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
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Sabadin PK, Malosetti M, Boer MP, Tardin FD, Santos FG, Guimarães CT, Gomide RL, Andrade CLT, Albuquerque PEP, Caniato FF, Mollinari M, Margarido GRA, Oliveira BF, Schaffert RE, Garcia AAF, van Eeuwijk FA, Magalhaes JV. Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1389-402. [PMID: 22297563 DOI: 10.1007/s00122-012-1795-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 01/05/2012] [Indexed: 05/25/2023]
Abstract
Managed environments in the form of well watered and water stressed trials were performed to study the genetic basis of grain yield and stay green in sorghum with the objective of validating previously detected QTL. As variations in phenology and plant height may influence QTL detection for the target traits, QTL for flowering time and plant height were introduced as cofactors in QTL analyses for yield and stay green. All but one of the flowering time QTL were detected near yield and stay green QTL. Similar co-localization was observed for two plant height QTL. QTL analysis for yield, using flowering time/plant height cofactors, led to yield QTL on chromosomes 2, 3, 6, 8 and 10. For stay green, QTL on chromosomes 3, 4, 8 and 10 were not related to differences in flowering time/plant height. The physical positions for markers in QTL regions projected on the sorghum genome suggest that the previously detected plant height QTL, Sb-HT9-1, and Dw2, in addition to the maturity gene, Ma5, had a major confounding impact on the expression of yield and stay green QTL. Co-localization between an apparently novel stay green QTL and a yield QTL on chromosome 3 suggests there is potential for indirect selection based on stay green to improve drought tolerance in sorghum. Our QTL study was carried out with a moderately sized population and spanned a limited geographic range, but still the results strongly emphasize the necessity of corrections for phenology in QTL mapping for drought tolerance traits in sorghum.
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Affiliation(s)
- P K Sabadin
- Embrapa Maize and Sorghum, Rod. MG 424, Km 65, Sete Lagoas, MG 35701-970, Brazil
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42
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Yan S, Wu X, Bean SR, Pedersen JF, Tesso T, Chen YR, Wang D. Evaluation of Waxy Grain Sorghum for Ethanol Production. Cereal Chem 2011. [DOI: 10.1094/cchem-04-11-0056] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Shuping Yan
- Department of Biological and Agricultural Engineering, Kansas State University, Manhattan, KS 66506
- Present address: C. W. Brabender Instrument, Inc., 50 E. Wesley Street, S. Hackensack, NJ 07606
| | - Xiaorong Wu
- Department of Biological and Agricultural Engineering, Kansas State University, Manhattan, KS 66506
| | - Scott R. Bean
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Center for Grain and Animal Health, Manhattan, KS 66502
| | - Jeffery F. Pedersen
- USDA-ARS, Grain, Forage, and Bioenergy Research Unit, Lincoln, NE 68583. Names are necessary to report factually on available data; however, USDA neither guarantees nor warrants the standard of the product, and the use of the name by the USDA implies no approval of the product to the exclusion of others that may also be suitable
| | - Tesfaye Tesso
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Yuanhong R. Chen
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Center for Grain and Animal Health, Manhattan, KS 66502
| | - Donghai Wang
- Department of Biological and Agricultural Engineering, Kansas State University, Manhattan, KS 66506
- Corresponding author. Phone: (785) 532-2919. Fax: (785) 532-5825. E-mail:
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43
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Jordan DR, Klein RR, Sakrewski KG, Henzell RG, Klein PE, Mace ES. Mapping and characterization of Rf 5: a new gene conditioning pollen fertility restoration in A1 and A2 cytoplasm in sorghum (Sorghum bicolor (L.) Moench). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:383-396. [PMID: 21487690 DOI: 10.1007/s00122-011-1591-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 03/31/2011] [Indexed: 05/30/2023]
Abstract
With an aim to further characterize the cytoplasmic male sterility-fertility restoration system in sorghum, a major fertility restoration gene was mapped along with a second locus capable of partial restoration of pollen fertility. The major fertility restoration gene, Rf(5), was located on sorghum chromosome SBI-05, and was capable of restoring pollen fertility in both A(1) and A(2) male sterile cytoplasms. Depending on the restorer parent, mapping populations exhibited fertility restoration phenotypes that ranged from nearly bimodal distribution due to the action of Rf(5), to a more normalized distribution reflecting the action of Rf(5) and additional modifier/partial restoration genes. A second fertility restoration locus capable of partially restoring pollen fertility in A(1) cytoplasm was localized to chromosome SBI-04. Unlike Rf(5), this modifier/partial restorer gene acting alone resulted in less than 10% seed set in both A(1) and A(2) cytoplasms, and modified the extent of restoration conditioned by the major restorer Rf(5) in A(1) cytoplasm. In examining the genomic regions spanning the Rf(5) locus, a cluster of pentatricopeptide gene family members with high homology to rice Rf (1) and sorghum Rf (2) were identified as potential candidates encoding Rf(5).
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Affiliation(s)
- D R Jordan
- Agri-Science Queensland, Hermitage Research Station, Yangan Road, Warwick, QLD 4370, Australia.
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44
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Mace ES, Jordan DR. Integrating sorghum whole genome sequence information with a compendium of sorghum QTL studies reveals uneven distribution of QTL and of gene-rich regions with significant implications for crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:169-91. [PMID: 21484332 DOI: 10.1007/s00122-011-1575-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 03/18/2011] [Indexed: 05/03/2023]
Abstract
A comprehensive analysis was conducted using 48 sorghum QTL studies published from 1995 to 2010 to make information from historical sorghum QTL experiments available in a form that could be more readily used by sorghum researchers and plant breeders. In total, 771 QTL relating to 161 unique traits from 44 studies were projected onto a sorghum consensus map. Confidence intervals (CI) of QTL were estimated so that valid comparisons could be made between studies. The method accounted for the number of lines used and the phenotypic variation explained by individual QTL from each study. In addition, estimated centimorgan (cM) locations were calculated for the predicted sorghum gene models identified in Phytozome (JGI GeneModels SBI v1.4) and compared with QTL distribution genome-wide, both on genetic linkage (cM) and physical (base-pair/bp) map scales. QTL and genes were distributed unevenly across the genome. Heterochromatic enrichment for QTL was observed, with approximately 22% of QTL either entirely or partially located in the heterochromatic regions. Heterochromatic gene enrichment was also observed based on their predicted cM locations on the sorghum consensus map, due to suppressed recombination in heterochromatic regions, in contrast to the euchromatic gene enrichment observed on the physical, sequence-based map. The finding of high gene density in recombination-poor regions, coupled with the association with increased QTL density, has implications for the development of more efficient breeding systems in sorghum to better exploit heterosis. The projected QTL information described, combined with the physical locations of sorghum sequence-based markers and predicted gene models, provides sorghum researchers with a useful resource for more detailed analysis of traits and development of efficient marker-assisted breeding strategies.
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Affiliation(s)
- E S Mace
- Department of Employment, Economic Development and Innovation, Hermitage Research Station, 604 Yangan Road, Warwick, QLD, 4370, Australia.
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Feuillet C, Leach JE, Rogers J, Schnable PS, Eversole K. Crop genome sequencing: lessons and rationales. TRENDS IN PLANT SCIENCE 2011; 16:77-88. [PMID: 21081278 DOI: 10.1016/j.tplants.2010.10.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 10/09/2010] [Accepted: 10/16/2010] [Indexed: 05/06/2023]
Abstract
2010 marks the 10th anniversary of the completion of the first plant genome sequence (Arabidopsis thaliana). Triggered by advancements in sequencing technologies, many crop genome sequences have been produced, with eight published since 2008. To date, however, only the rice (Oryza sativa) genome sequence has been finished to a quality level similar to that of the Arabidopsis sequence. This trend to produce draft genomes could affect the ability of researchers to address biological questions of speciation and recent evolution or to link sequence variation accurately to phenotypes. Here, we review the current crop genome sequencing activities, discuss how variability in sequence quality impacts utility for different studies and provide a perspective for a paradigm shift in selecting crops for sequencing in the future.
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Affiliation(s)
- Catherine Feuillet
- Institut National de la Recherche Agronomique-Université Blaise Pascal-UMR1095-Domaine de Crouel, 63100 Clermont-Ferrand, France.
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