Dataset Information

Genome-Wide Association Studies for Five Forage Quality-Related Traits in Sorghum (Sorghum bicolor L.).

ABSTRACT: Understanding the genetic function of the forage quality-related traits, including crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose (HC), and cellulose (CL) contents, is essential for the identification of forage quality genes and selection of effective molecular markers in sorghum. In this study, we genotyped 245 sorghum accessions by 85,585 single-nucleotide polymorphisms (SNPs) and obtained the phenotypic data from four environments. The SNPs and phenotypic data were applied to multi-locus genome-wide association studies (GWAS) with the mrMLM software. A total of 42 SNPs were identified to be associated with the five forage quality-related traits. Moreover, three and two quantitative trait nucleotides (QTNs) were simultaneously detected among them by three and two multi-locus methods, respectively. One QTN on chromosome 5 was found to be associated simultaneously with CP, NDF, and ADF. Furthermore, 3, 2, 2, 5, and 2 candidate genes were identified to be responsible for CP, NDF, ADF, HC, and CL contents, respectively. These results provided insightful information of the forage quality-related traits and would facilitate the genetic improvement of sorghum forage quality in the future.

SUBMITTER: Li J

PROVIDER: S-EPMC6111974 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Genome-Wide Association Studies for Five Forage Quality-Related Traits in Sorghum (<i>Sorghum bicolor</i> L.).

Li Jieqin J Tang Weijie W Zhang Ya-Wen YW Chen Kai-Ning KN Wang Chenchen C Liu Yanlong Y Zhan Qiuwen Q Wang Chunming C Wang Shi-Bo SB Xie Shang-Qian SQ Wang Lihua L

Frontiers in plant science 20180821

Understanding the genetic function of the forage quality-related traits, including crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose (HC), and cellulose (CL) contents, is essential for the identification of forage quality genes and selection of effective molecular markers in sorghum. In this study, we genotyped 245 sorghum accessions by 85,585 single-nucleotide polymorphisms (SNPs) and obtained the phenotypic data from four environments. The SNPs and ph ...[more]

PMID: 30186292

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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:The efficient use of sorghum as a renewable energy source requires high biomass yields and reduced agricultural inputs. Hybridization of Sorghum bicolor with wild Sorghum halepense can help meet both requirements, generating high-yielding and environment friendly perennial sorghum cultivars. Selection efficiency, however, needs to be improved to exploit the genetic potential of the derived recombinant lines and remove weedy and other wild traits. In this work, we present the results from a Genome-Wide Association Study conducted on a diversity panel made up of S. bicolor and an advanced population derived from S. bicolor × S. halepense multi-parent crosses. The objective was to identify genetic loci controlling biomass yield and biomass-relevant traits for breeding purposes. Plants were phenotyped during four consecutive years for dry biomass yield, dry mass fraction of fresh material, plant height and plant maturity. A genotyping-by-sequencing approach was implemented to obtain 92,383 high quality SNP markers used in this work. Significant marker-trait associations were uncovered across eight of the ten sorghum chromosomes, with two main hotspots near the end of chromosomes 7 and 9, in proximity of dwarfing genes Dw1 and Dw3. No significant marker was found on chromosomes 2 and 4. A large number of significant marker loci associated with biomass yield and biomass-relevant traits showed minor effects on respective plant characteristics, with the exception of seven loci on chromosomes 3, 8, and 9 that explained 5.2-7.8% of phenotypic variability in dry mass yield, dry mass fraction of fresh material, and maturity, and a major effect (R 2 = 16.2%) locus on chromosome 1 for dry mass fraction of fresh material which co-localized with a zinc-finger homeodomain protein possibly involved in the expression of the D (Dry stalk) locus. These markers and marker haplotypes identified in this work are expected to boost marker-assisted selection in sorghum breeding.

Project description:Genetic progress for forage quality has been poor in alfalfa (Medicago sativa L.), the most-grown forage legume worldwide. This study aimed at exploring opportunities for marker-assisted selection (MAS) and genomic selection of forage quality traits based on breeding values of parent plants. Some 154 genotypes from a broadly-based reference population were genotyped by genotyping-by-sequencing (GBS), and phenotyped for leaf-to-stem ratio, leaf and stem contents of protein, neutral detergent fiber (NDF) and acid detergent lignin (ADL), and leaf and stem NDF digestibility after 24 hours (NDFD), of their dense-planted half-sib progenies in three growing conditions (summer harvest, full irrigation; summer harvest, suspended irrigation; autumn harvest). Trait-marker analyses were performed on progeny values averaged over conditions, owing to modest germplasm × condition interaction. Genomic selection exploited 11,450 polymorphic SNP markers, whereas a subset of 8,494 M. truncatula-aligned markers were used for a genome-wide association study (GWAS). GWAS confirmed the polygenic control of quality traits and, in agreement with phenotypic correlations, indicated substantially different genetic control of a given trait in stems and leaves. It detected several SNPs in different annotated genes that were highly linked to stem protein content. Also, it identified a small genomic region on chromosome 8 with high concentration of annotated genes associated with leaf ADL, including one gene probably involved in the lignin pathway. Three genomic selection models, i.e., Ridge-regression BLUP, Bayes B and Bayesian Lasso, displayed similar prediction accuracy, whereas SVR-lin was less accurate. Accuracy values were moderate (0.3-0.4) for stem NDFD and leaf protein content, modest for leaf ADL and NDFD, and low to very low for the other traits. Along with previous results for the same germplasm set, this study indicates that GBS data can be exploited to improve both quality traits (by genomic selection or MAS) and forage yield.

Dataset Information

Genome-Wide Association Studies for Five Forage Quality-Related Traits in Sorghum (Sorghum bicolor L.).

Publications

Genome-Wide Association Studies for Five Forage Quality-Related Traits in Sorghum (<i>Sorghum bicolor</i> L.).

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