1
|
Zhang Z, Gomes Viana JP, Zhang B, Walden KKO, Müller Paul H, Moose SP, Morris GP, Daum C, Barry KW, Shakoor N, Hudson ME. Major impacts of widespread structural variation on sorghum. Genome Res 2024; 34:286-299. [PMID: 38479835 PMCID: PMC10984582 DOI: 10.1101/gr.278396.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/22/2024] [Indexed: 03/22/2024]
Abstract
Genetic diversity is critical to crop breeding and improvement, and dissection of the genomic variation underlying agronomic traits can both assist breeding and give insight into basic biological mechanisms. Although recent genome analyses in plants reveal many structural variants (SVs), most current studies of crop genetic variation are dominated by single-nucleotide polymorphisms (SNPs). The extent of the impact of SVs on global trait variation, as well as their utility in genome-wide selection, is not yet understood. In this study, we built an SV data set based on whole-genome resequencing of diverse sorghum lines (n = 363), validated the correlation of photoperiod sensitivity and variety type, and identified SV hotspots underlying the divergent evolution of cellulosic and sweet sorghum. In addition, we showed the complementary contribution of SVs for heritability of traits related to sorghum adaptation. Importantly, inclusion of SV polymorphisms in association studies revealed genotype-phenotype associations not observed with SNPs alone. Three-way genome-wide association studies (GWAS) based on whole-genome SNP, SV, and integrated SNP + SV data sets showed substantial associations between SVs and sorghum traits. The addition of SVs to GWAS substantially increased heritability estimates for some traits, indicating their important contribution to functional allelic variation at the genome level. Our discovery of the widespread impacts of SVs on heritable gene expression variation could render a plausible mechanism for their disproportionate impact on phenotypic variation. This study expands our knowledge of SVs and emphasizes the extensive impacts of SVs on sorghum.
Collapse
Affiliation(s)
- Zhihai Zhang
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Joao Paulo Gomes Viana
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Bosen Zhang
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kimberly K O Walden
- High Performance Computing in Biology, Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Hans Müller Paul
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Stephen P Moose
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Geoffrey P Morris
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Chris Daum
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kerrie W Barry
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Nadia Shakoor
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Matthew E Hudson
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA;
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| |
Collapse
|
2
|
Kang X, Gao W, Cui B, El-Aty AMA. Structure and genetic regulation of starch formation in sorghum (Sorghum bicolor (L.) Moench) endosperm: A review. Int J Biol Macromol 2023; 239:124315. [PMID: 37023877 DOI: 10.1016/j.ijbiomac.2023.124315] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/08/2023]
Abstract
This review focuses on the structure and genetic regulation of starch formation in sorghum (Sorghum bicolor (L.) Moench) endosperm. Sorghum is an important cereal crop that is well suited to grow in regions with high temperatures and limited water resources due to its C4 metabolism. The endosperm of sorghum kernels is a rich source of starch, which is composed of two main components: amylose and amylopectin. The synthesis of starch in sorghum endosperm involves multiple enzymatic reactions, which are regulated by complex genetic and environmental factors. Recent research has identified several genes involved in the regulation of starch synthesis in sorghum endosperm. In addition, the structure and properties of sorghum starch can also be influenced by environmental factors such as temperature, water availability, and soil nutrients. A better understanding of the structure and genetic regulation of starch formation in sorghum endosperm can have important implications for the development of sorghum-based products with improved quality and nutritional value. This review provides a comprehensive summary of the current knowledge on the structure and genetic regulation of starch formation in sorghum endosperm and highlights the potential for future research to further improve our understanding of this important process.
Collapse
Affiliation(s)
- Xuemin Kang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, Shandong 250353, China; Department of Food Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Wei Gao
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, Shandong 250353, China
| | - Bo Cui
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; School of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, Shandong 250353, China; Department of Food Science and Engineering, Shandong Agricultural University, Taian 271018, China.
| | - A M Abd El-Aty
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan 250353, China; Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt; Department of Medical Pharmacology, Medical Faculty, Ataturk University, 25240 Erzurum, Turkey
| |
Collapse
|
3
|
Enyew M, Feyissa T, Carlsson AS, Tesfaye K, Hammenhag C, Geleta M. Genetic Diversity and Population Structure of Sorghum [ Sorghum Bicolor (L.) Moench] Accessions as Revealed by Single Nucleotide Polymorphism Markers. FRONTIERS IN PLANT SCIENCE 2022; 12:799482. [PMID: 35069657 PMCID: PMC8766336 DOI: 10.3389/fpls.2021.799482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/03/2021] [Indexed: 05/17/2023]
Abstract
Ethiopia is the center of origin for sorghum [Sorghum bicolor (L.) Moench], where the distinct agro-ecological zones significantly contributed to the genetic diversity of the crops. A large number of sorghum landrace accessions have been conserved ex situ. Molecular characterization of this diverse germplasm can contribute to its efficient conservation and utilization in the breeding programs. This study aimed to investigate the genetic diversity of Ethiopian sorghum using gene-based single nucleotide polymorphism (SNP) markers. In total, 359 individuals representing 24 landrace accessions were genotyped using 3,001 SNP markers. The SNP markers had moderately high polymorphism information content (PIC = 0.24) and gene diversity (H = 0.29), on average. This study revealed 48 SNP loci that were significantly deviated from Hardy-Weinberg equilibrium with excess heterozygosity and 13 loci presumed to be under selection (P < 0.01). The analysis of molecular variance (AMOVA) determined that 35.5% of the total variation occurred within and 64.5% among the accessions. Similarly, significant differentiations were observed among geographic regions and peduncle shape-based groups. In the latter case, accessions with bent peduncles had higher genetic variation than those with erect peduncles. More alleles that are private were found in the eastern region than in the other regions of the country, suggesting a good in situ conservation status in the east. Cluster, principal coordinates (PCoA), and STRUCTURE analyses revealed distinct accession clusters. Hence, crossbreeding genotypes from different clusters and evaluating their progenies for desirable traits is advantageous. The exceptionally high heterozygosity observed in accession SB4 and SB21 from the western geographic region is an intriguing finding of this study, which merits further investigation.
Collapse
Affiliation(s)
- Muluken Enyew
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Tileye Feyissa
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Anders S. Carlsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| |
Collapse
|
4
|
de Oliveira LDL, de Oliveira GT, de Alencar ER, Queiroz VAV, de Alencar Figueiredo LF. Physical, chemical, and antioxidant analysis of sorghum grain and flour from five hybrids to determine the drivers of liking of gluten-free sorghum breads. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
5
|
Nayak SN, Aravind B, Malavalli SS, Sukanth BS, Poornima R, Bharati P, Hefferon K, Kole C, Puppala N. Omics Technologies to Enhance Plant Based Functional Foods: An Overview. Front Genet 2021; 12:742095. [PMID: 34858472 PMCID: PMC8631721 DOI: 10.3389/fgene.2021.742095] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022] Open
Abstract
Functional foods are natural products of plants that have health benefits beyond necessary nutrition. Functional foods are abundant in fruits, vegetables, spices, beverages and some are found in cereals, millets, pulses and oilseeds. Efforts to identify functional foods in our diet and their beneficial aspects are limited to few crops. Advances in sequencing and availability of different omics technologies have given opportunity to utilize these tools to enhance the functional components of the foods, thus ensuring the nutritional security. Integrated omics approaches including genomics, transcriptomics, proteomics, metabolomics coupled with artificial intelligence and machine learning approaches can be used to improve the crops. This review provides insights into omics studies that are carried out to find the active components and crop improvement by enhancing the functional compounds in different plants including cereals, millets, pulses, oilseeds, fruits, vegetables, spices, beverages and medicinal plants. There is a need to characterize functional foods that are being used in traditional medicines, as well as utilization of this knowledge to improve the staple foods in order to tackle malnutrition and hunger more effectively.
Collapse
Affiliation(s)
- Spurthi N. Nayak
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - B. Aravind
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Sachin S. Malavalli
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - B. S. Sukanth
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - R. Poornima
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Pushpa Bharati
- Department of Food Science and Nutrition, University of Agricultural Sciences, Dharwad, India
| | - Kathleen Hefferon
- Department of Microbiology, Cornell University, Ithaca, NY, United States
| | - Chittaranjan Kole
- President, International Phytomedomics and Nutriomics Consortium (ipnc.info), Daejeon, South Korea
| | - Naveen Puppala
- New Mexico State University-Agricultural Science Center at Clovis, New Mexico, NM, United States
| |
Collapse
|
6
|
Fox G, Nugusu Y, Nida H, Tedessa T, McLean G, Jordan D. Evaluation of variation in Ethiopian sorghum injera quality with new imaging techniques. Cereal Chem 2020. [DOI: 10.1002/cche.10252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Glen Fox
- Queensland Alliance for Agriculture and Food Innovation The University of Queensland St Lucia Qld Australia
- Department of Food Science Stellenbosch University Stellenbosch South Africa
| | - Yohannes Nugusu
- Ethiopian Institute of Agricultural Research Melkasa Ethiopia
| | - Habte Nida
- Ethiopian Institute of Agricultural Research Melkasa Ethiopia
| | - Taye Tedessa
- Ethiopian Institute of Agricultural Research Melkasa Ethiopia
| | - Greg McLean
- Department of Agriculture and Fisheries Toowoomba Qld Australia
| | - David Jordan
- Queensland Alliance for Agriculture and Food Innovation The University of Queensland St Lucia Qld Australia
| |
Collapse
|
7
|
Guindo D, Teme N, Vaksmann M, Doumbia M, Vilmus I, Guitton B, Sissoko A, Mestres C, Davrieux F, Fliedel G, Kouressy M, Courtois B, Rami JF. Quantitative trait loci for sorghum grain morphology and quality traits: Toward breeding for a traditional food preparation of West-Africa. J Cereal Sci 2019. [DOI: 10.1016/j.jcs.2018.11.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
8
|
Perrier L, Rouan L, Jaffuel S, Clément-Vidal A, Roques S, Soutiras A, Baptiste C, Bastianelli D, Fabre D, Dubois C, Pot D, Luquet D. Plasticity of Sorghum Stem Biomass Accumulation in Response to Water Deficit: A Multiscale Analysis from Internode Tissue to Plant Level. FRONTIERS IN PLANT SCIENCE 2017; 8:1516. [PMID: 28919904 PMCID: PMC5585773 DOI: 10.3389/fpls.2017.01516] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/17/2017] [Indexed: 05/20/2023]
Abstract
Sorghum is increasingly used as a biomass crop worldwide. Its genetic diversity provides a large range of stem biochemical composition suitable for various end-uses as bioenergy or forage. Its drought tolerance enables it to reasonably sustain biomass production under water limited conditions. However, drought effect on the accumulation of sorghum stem biomass remains poorly understood which limits progress in crop improvement and management. This study aimed at identifying the morphological, biochemical and histological traits underlying biomass accumulation in the sorghum stem and its plasticity in response to water deficit. Two hybrids (G1, G4) different in stem biochemical composition (G4, more lignified, less sweet) were evaluated during 2 years in the field in Southern France, under two water treatments differentiated during stem elongation (irrigated; 1 month dry-down until an average soil water deficit of -8.85 bars). Plant phenology was observed weekly. At the end of the water treatment and at final harvest, plant height, stem and leaf dry-weight and the size, biochemical composition and tissue histology of internodes at 2-4 positions along the stem were measured. Stem biomass accumulation was significantly reduced by drought (in average 42% at the end of the dry-down). This was due to the reduction of the length, but not diameter, of the internodes expanded during water deficit. These internodes had more soluble sugar but lower lignin and cellulose contents. This was associated with a decrease of the areal proportion of lignified cell wall in internode outer zone whereas the areal proportion of this zone was not affected. All internodes for a given genotype and environment followed a common histochemical dynamics. Hemicellulose content and the areal proportion of inner vs. outer internode tissues were set up early during internode growth and were not drought responsive. G4 exhibited a higher drought sensitivity than G1 for plant height only. At final harvest, the stem dry weight was only 18% lower in water deficit (re-watered) compared to well-watered treatment and internodes growing during re-watering were similar to those on the well-watered plants. These results are being valorized to refine the phenotyping of sorghum diversity panels and breeding populations.
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Genetic architecture of kernel composition in global sorghum germplasm. BMC Genomics 2017; 18:15. [PMID: 28056770 PMCID: PMC5217548 DOI: 10.1186/s12864-016-3403-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/09/2016] [Indexed: 12/30/2022] Open
Abstract
Background Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop for dryland areas in the United States and for small-holder farmers in Africa. Natural variation of sorghum grain composition (protein, fat, and starch) between accessions can be used for crop improvement, but the genetic controls are still unresolved. The goals of this study were to quantify natural variation of sorghum grain composition and to identify single-nucleotide polymorphisms (SNPs) associated with variation in grain composition concentrations. Results In this study, we quantified protein, fat, and starch in a global sorghum diversity panel using near-infrared spectroscopy (NIRS). Protein content ranged from 8.1 to 18.8%, fat content ranged from 1.0 to 4.3%, and starch content ranged from 61.7 to 71.1%. Durra and bicolor-durra sorghum from Ethiopia and India had the highest protein and fat and the lowest starch content, while kafir sorghum from USA, India, and South Africa had the lowest protein and the highest starch content. Genome-wide association studies (GWAS) identified quantitative trait loci (QTL) for sorghum protein, fat, and starch. Previously published RNAseq data was used to identify candidate genes within a GWAS QTL region. A putative alpha-amylase 3 gene, which has previously been shown to be associated with grain composition traits, was identified as a strong candidate for protein and fat variation. Conclusions We identified promising sources of genetic material for manipulation of grain composition traits, and several loci and candidate genes that may control sorghum grain composition. This survey of grain composition in sorghum germplasm and identification of protein, fat, and starch QTL contributes to our understanding of the genetic basis of natural variation in sorghum grain nutritional traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3403-x) contains supplementary material, which is available to authorized users.
Collapse
|
11
|
Campbell BC, Gilding EK, Mace ES, Tai S, Tao Y, Prentis PJ, Thomelin P, Jordan DR, Godwin ID. Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:2240-2253. [PMID: 27155090 PMCID: PMC5103234 DOI: 10.1111/pbi.12578] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 05/02/2016] [Indexed: 05/04/2023]
Abstract
Next-generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either 'Landraces' or 'Wild and Weedy' genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP-glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well-characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways.
Collapse
Affiliation(s)
- Bradley C. Campbell
- School of Agriculture and Food SciencesThe University of QueenslandBrisbaneQldAustralia
| | - Edward K. Gilding
- School of Agriculture and Food SciencesThe University of QueenslandBrisbaneQldAustralia
| | - Emma S. Mace
- Department of Agriculture and Fisheries (DAF)WarwickQldAustralia
| | | | - Yongfu Tao
- Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandWarwickQldAustralia
| | - Peter J. Prentis
- Science and Engineering FacultyQueensland University of Technology (QUT)BrisbaneQldAustralia
| | - Pauline Thomelin
- Australian Centre for Plant Functional GenomicsGlen OsmondSAAustralia
| | - David R. Jordan
- Queensland Alliance for Agriculture and Food InnovationThe University of QueenslandWarwickQldAustralia
| | - Ian D. Godwin
- School of Agriculture and Food SciencesThe University of QueenslandBrisbaneQldAustralia
| |
Collapse
|
12
|
Singh AK, Singh R, Subramani R, Kumar R, Wankhede DP. Molecular Approaches to Understand Nutritional Potential of Coarse Cereals. Curr Genomics 2016; 17:177-92. [PMID: 27252585 PMCID: PMC4869005 DOI: 10.2174/1389202917666160202215308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 01/01/2023] Open
Abstract
Coarse grains are important group of crops that constitutes staple food for large population residing primarily in the arid and semi-arid regions of the world. Coarse grains are designated as nutri-cereals as they are rich in essential amino acids, minerals and vitamins. In spite of having several nutritional virtues in coarse grain as mentioned above, there is still scope for improvement in quality parameters such as cooking qualities, modulation of nutritional constituents and reduction or elimination of anti-nutritional factors. Besides its use in traditional cooking, coarse grains have been used mainly in the weaning food preparation and other malted food production. Improvement in quality parameters will certainly increase consumer's preference for coarse grains and increase their demand. The overall genetic gain in quality traits of economic importance in the cultivated varieties will enhance their industrial value and simultaneously increase income of farmers growing these varieties. The urgent step for improvement of quality traits in coarse grains requires a detailed understanding of molecular mechanisms responsible for varied level of different nutritional contents in different genotypes of these crops. In this review we have discussed the progresses made in understanding of coarse grain biology with various omics tool coupled with modern breeding approaches and the current status with regard to our effort towards dissecting traits related to improvement of quality and nutritional constituents of grains.
Collapse
Affiliation(s)
- Amit Kumar Singh
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rajkumar Subramani
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rajesh Kumar
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | | |
Collapse
|
13
|
Sehgal D, Singh R, Rajpal VR. Quantitative Trait Loci Mapping in Plants: Concepts and Approaches. MOLECULAR BREEDING FOR SUSTAINABLE CROP IMPROVEMENT 2016. [DOI: 10.1007/978-3-319-27090-6_2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
14
|
Adeyanju A, Little C, Yu J, Tesso T. Genome-Wide Association Study on Resistance to Stalk Rot Diseases in Grain Sorghum. G3 (BETHESDA, MD.) 2015; 5:1165-75. [PMID: 25882062 PMCID: PMC4478546 DOI: 10.1534/g3.114.016394] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/06/2015] [Indexed: 02/08/2023]
Abstract
Stalk rots are important biotic constraints to sorghum production worldwide. Several pathogens may be associated with the disease, but Macrophomina phaseolina and Fusarium thapsinum are recognized as the major causal organisms. The diseases become more aggressive when drought and high-temperature stress occur during grain filling. Progress in genetic improvement efforts has been slow due to lack of effective phenotyping protocol and the strong environmental effect on disease incidence and severity. Deployment of modern molecular tools is expected to accelerate efforts to develop resistant hybrids. This study was aimed at identifying genomic regions associated with resistance to both causal organisms. A sorghum diversity panel consisting of 300 genotypes assembled from different parts of the world was evaluated for response to infection by both pathogens. Community resources of 79,132 single nucleotide polymorphic (SNP) markers developed on the panel were used in association studies using a multi-locus mixed model to map loci associated with stalk rot resistance. Adequate genetic variation was observed for resistance to both pathogens. Structure analysis grouped the genotypes into five subpopulations primarily based on the racial category of the genotypes. Fourteen loci and a set of candidate genes appear to be involved in connected functions controlling plant defense response. However, each associated SNP had relatively small effect on the traits, accounting for 19-30% of phenotypic variation. Linkage disequilibrium analyses suggest that significant SNPs are genetically independent. Estimation of frequencies of associated alleles revealed that durra and caudatum subpopulations were enriched for resistant alleles, but the results suggest complex molecular mechanisms underlying resistance to both pathogens.
Collapse
Affiliation(s)
- Adedayo Adeyanju
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506
| | - Christopher Little
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
| | - Tesfaye Tesso
- Department of Agronomy, Kansas State University, Manhattan, Kansas 66506
| |
Collapse
|
15
|
Montilla-Bascón G, Rispail N, Sánchez-Martín J, Rubiales D, Mur LAJ, Langdon T, Howarth CJ, Prats E. Genome-wide association study for crown rust (Puccinia coronata f. sp. avenae) and powdery mildew (Blumeria graminis f. sp. avenae) resistance in an oat (Avena sativa) collection of commercial varieties and landraces. FRONTIERS IN PLANT SCIENCE 2015; 6:103. [PMID: 25798140 PMCID: PMC4350391 DOI: 10.3389/fpls.2015.00103] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/08/2015] [Indexed: 05/19/2023]
Abstract
Diseases caused by crown rust (Puccinia coronata f. sp. avenae) and powdery mildew (Blumeria graminis f. sp. avenae) are among the most important constraints for the oat crop. Breeding for resistance is one of the most effective, economical, and environmentally friendly means to control these diseases. The purpose of this work was to identify elite alleles for rust and powdery mildew resistance in oat by association mapping to aid selection of resistant plants. To this aim, 177 oat accessions including white and red oat cultivars and landraces were evaluated for disease resistance and further genotyped with 31 simple sequence repeat and 15,000 Diversity Arrays Technology (DArT) markers to reveal association with disease resistance traits. After data curation, 1712 polymorphic markers were considered for association analysis. Principal component analysis and a Bayesian clustering approach were applied to infer population structure. Five different general and mixed linear models accounting for population structure and/or kinship corrections and two different statistical tests were carried out to reduce false positive. Five markers, two of them highly significant in all models tested were associated with rust resistance. No strong association between any marker and powdery mildew resistance at the seedling stage was identified. However, one DArT sequence, oPt-5014, was strongly associated with powdery mildew resistance in adult plants. Overall, the markers showing the strongest association in this study provide ideal candidates for further studies and future inclusion in strategies of marker-assisted selection.
Collapse
Affiliation(s)
- Gracia Montilla-Bascón
- Institute for Sustainable Agriculture – Consejo Superior de Investigaciones CientíficasCórdoba, Spain
| | - Nicolas Rispail
- Institute for Sustainable Agriculture – Consejo Superior de Investigaciones CientíficasCórdoba, Spain
| | - Javier Sánchez-Martín
- Institute for Sustainable Agriculture – Consejo Superior de Investigaciones CientíficasCórdoba, Spain
| | - Diego Rubiales
- Institute for Sustainable Agriculture – Consejo Superior de Investigaciones CientíficasCórdoba, Spain
| | - Luis A. J. Mur
- Institute of Biological, Environmental and Rural Sciences, University of AberystwythAberystwyth, UK
| | - Tim Langdon
- Institute of Biological, Environmental and Rural Sciences, University of AberystwythAberystwyth, UK
| | - Catherine J. Howarth
- Institute of Biological, Environmental and Rural Sciences, University of AberystwythAberystwyth, UK
| | - Elena Prats
- Institute for Sustainable Agriculture – Consejo Superior de Investigaciones CientíficasCórdoba, Spain
- *Correspondence: Elena Prats, Institute for Sustainable Agriculture – Consejo Superior de Investigaciones Científicas, Apartado 4084, E-14080 Córdoba, Spain e-mail:
| |
Collapse
|
16
|
Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE, Harriman J, Glaubitz JC, Buckler ES, Kresovich S. Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci U S A 2013; 110:453-8. [PMID: 23267105 PMCID: PMC3545811 DOI: 10.1073/pnas.1215985110] [Citation(s) in RCA: 459] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Accelerating crop improvement in sorghum, a staple food for people in semiarid regions across the developing world, is key to ensuring global food security in the context of climate change. To facilitate gene discovery and molecular breeding in sorghum, we have characterized ~265,000 single nucleotide polymorphisms (SNPs) in 971 worldwide accessions that have adapted to diverse agroclimatic conditions. Using this genome-wide SNP map, we have characterized population structure with respect to geographic origin and morphological type and identified patterns of ancient crop diffusion to diverse agroclimatic regions across Africa and Asia. To better understand the genomic patterns of diversification in sorghum, we quantified variation in nucleotide diversity, linkage disequilibrium, and recombination rates across the genome. Analyzing nucleotide diversity in landraces, we find evidence of selective sweeps around starch metabolism genes, whereas in landrace-derived introgression lines, we find introgressions around known height and maturity loci. To identify additional loci underlying variation in major agroclimatic traits, we performed genome-wide association studies (GWAS) on plant height components and inflorescence architecture. GWAS maps several classical loci for plant height, candidate genes for inflorescence architecture. Finally, we trace the independent spread of multiple haplotypes carrying alleles for short stature or long inflorescence branches. This genome-wide map of SNP variation in sorghum provides a basis for crop improvement through marker-assisted breeding and genomic selection.
Collapse
Affiliation(s)
- Geoffrey P Morris
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Bouchet S, Pot D, Deu M, Rami JF, Billot C, Perrier X, Rivallan R, Gardes L, Xia L, Wenzl P, Kilian A, Glaszmann JC. Genetic structure, linkage disequilibrium and signature of selection in Sorghum: lessons from physically anchored DArT markers. PLoS One 2012; 7:e33470. [PMID: 22428056 PMCID: PMC3302775 DOI: 10.1371/journal.pone.0033470] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 02/09/2012] [Indexed: 11/19/2022] Open
Abstract
Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r(2) decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod.
Collapse
Affiliation(s)
| | - David Pot
- UMR AGAP, CIRAD, Montpellier, France
| | | | | | | | | | | | | | - Ling Xia
- Diversity Arrays Technology Pty Ltd., Yarralumla, Australia
| | - Peter Wenzl
- Diversity Arrays Technology Pty Ltd., Yarralumla, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd., Yarralumla, Australia
| | | |
Collapse
|
18
|
Hill H, Slade Lee L, Henry RJ. Variation in sorghum starch synthesis genes associated with differences in starch phenotype. Food Chem 2012. [DOI: 10.1016/j.foodchem.2011.08.057] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|