Dataset Information

Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor).

ABSTRACT: BACKGROUND:Sorghum (Sorghum bicolor) is globally produced as a source of food, feed, fiber and fuel. Grain and sweet sorghums differ in a number of important traits, including stem sugar and juice accumulation, plant height as well as grain and biomass production. The first whole genome sequence of a grain sorghum is available, but additional genome sequences are required to study genome-wide and intraspecific variation for dissecting the genetic basis of these important traits and for tailor-designed breeding of this important C4 crop. RESULTS:We resequenced two sweet and one grain sorghum inbred lines, and identified a set of nearly 1,500 genes differentiating sweet and grain sorghum. These genes fall into ten major metabolic pathways involved in sugar and starch metabolisms, lignin and coumarin biosynthesis, nucleic acid metabolism, stress responses and DNA damage repair. In addition, we uncovered 1,057,018 SNPs, 99,948 indels of 1 to 10 bp in length and 16,487 presence/absence variations as well as 17,111 copy number variations. The majority of the large-effect SNPs, indels and presence/absence variations resided in the genes containing leucine rich repeats, PPR repeats and disease resistance R genes possessing diverse biological functions or under diversifying selection, but were absent in genes that are essential for life. CONCLUSIONS:This is a first report of the identification of genome-wide patterns of genetic variation in sorghum. High-density SNP and indel markers reported here will be a valuable resource for future gene-phenotype studies and the molecular breeding of this important crop and related species.

SUBMITTER: Zheng LY

PROVIDER: S-EPMC3334600 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature

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Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor).

Zheng Lei-Ying LY Guo Xiao-Sen XS He Bing B Sun Lian-Jun LJ Peng Yao Y Dong Shan-Shan SS Liu Teng-Fei TF Jiang Shuye S Ramachandran Srinivasan S Liu Chun-Ming CM Jing Hai-Chun HC

Genome biology 20111121 11

<h4>Background</h4>Sorghum (Sorghum bicolor) is globally produced as a source of food, feed, fiber and fuel. Grain and sweet sorghums differ in a number of important traits, including stem sugar and juice accumulation, plant height as well as grain and biomass production. The first whole genome sequence of a grain sorghum is available, but additional genome sequences are required to study genome-wide and intraspecific variation for dissecting the genetic basis of these important traits and for t ...[more]

PMID: 22104744

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Project description:BACKGROUND:In sorghum (Sorghum bicolor), one paramount breeding objective is to increase grain quality. The nutritional quality and end use value of sorghum grains are primarily influenced by the proportions of tannins, starch and proteins, but the genetic basis of these grain quality traits remains largely unknown. This study aimed to dissect the natural variation of sorghum grain quality traits and identify the underpinning genetic loci by genome-wide association study. RESULTS:Levels of starch, tannins and 17 amino acids were quantified in 196 diverse sorghum inbred lines, and 44 traits based on known metabolic pathways and biochemical interactions amongst the 17 amino acids calculated. A Genome-wide association study (GWAS) with 3,512,517 SNPs from re-sequencing data identified 14, 15 and 711 significant SNPs which represented 14, 14, 492 genetic loci associated with levels of tannins, starch and amino acids in sorghum grains, respectively. Amongst these significant SNPs, two SNPs were associated with tannin content on chromosome 4 and colocalized with three previously identified loci for Tannin1, and orthologs of Zm1 and TT16 genes. One SNP associated with starch content colocalized with sucrose phosphate synthase gene. Furthermore, homologues of opaque1 and opaque2 genes associated with amino acid content were identified. Using the KEGG pathway database, six and three candidate genes of tannins and starch were mapped into 12 and 3 metabolism pathways, respectively. Thirty-four candidate genes were mapped into 16 biosynthetic and catabolic pathways of amino acids. We finally reconstructed the biosynthetic pathways for aspartate and branched-chain amino acids based on 15 candidate genes identified in this study. CONCLUSION:Promising candidate genes associated with grain quality traits have been identified in the present study. Some of them colocalized with previously identified genetic regions, but novel candidate genes involved in various metabolic pathways which influence grain quality traits have been dissected. Our study acts as an entry point for further validation studies to elucidate the complex mechanisms controlling grain quality traits such as tannins, starch and amino acids in sorghum.

Project description:WRKY transcription factors regulate diverse biological processes in plants, including abiotic and biotic stress responses, and constitute one of the largest transcription factor families in higher plants. Although the past decade has seen significant progress towards identifying and functionally characterizing WRKY genes in diverse species, little is known about the WRKY family in sorghum (Sorghum bicolor (L.) moench). Here we report the comprehensive identification of 94 putative WRKY transcription factors (SbWRKYs). The SbWRKYs were divided into three groups (I, II, and III), with those in group II further classified into five subgroups (IIa-IIe), based on their conserved domains and zinc finger motif types. WRKYs from the model plant Arabidopsis (Arabidopsis thaliana) were used for the phylogenetic analysis of all SbWRKY genes. Motif analysis showed that all SbWRKYs contained either one or two WRKY domains and that SbWRKYs within the same group had similar motif compositions. SbWRKY genes were located on all 10 sorghum chromosomes, and some gene clusters and two tandem duplications were detected. SbWRKY gene structure analysis showed that they contained 0-7 introns, with most SbWRKY genes consisting of two introns and three exons. Gene ontology (GO) annotation functionally categorized SbWRKYs under cellular components, molecular functions and biological processes. A cis-element analysis showed that all SbWRKYs contain at least one stress response-related cis-element. We exploited publicly available microarray datasets to analyze the expression profiles of 78 SbWRKY genes at different growth stages and in different tissues. The induction of SbWRKYs by different abiotic stresses hinted at their potential involvement in stress responses. qRT-PCR analysis revealed different expression patterns for SbWRKYs during drought stress. Functionally characterized WRKY genes in Arabidopsis and other species will provide clues for the functional characterization of putative orthologs in sorghum. Thus, the present study delivers a solid foundation for future functional studies of SbWRKY genes and their roles in the response to critical stresses such as drought.

Dataset Information

Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor).

Publications

Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor).

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