Multi-locus genome-wide association mapping for major agronomic and yield-related traits in sorghum (Sorghum bicolor (L.) moench) landraces.

IF 3.5 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Addisu Getahun, Admas Alemu, Habte Nida, Adugna Abdi Woldesemayat
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引用次数: 0

Abstract

Background: Sorghum is a vital cereal crop for over 750 million people, ranking 5th globally. It has multiple purposes, including food, feed, and biofuels, and is essential in Ethiopia, which has a rich genetic diversity of various agroecological zones.

Objective: Explore marker-trait associations (MTAs) to identify quantitative trait nucleotides (QTNs) and new candidate genes associated with agronomic and yield contributing traits in Ethiopian sorghum landraces using multi-locus GWAS models to assist the genomic-assisted breeding strategies.

Method: This study investigates the genetic basis of agronomic traits in Ethiopian sorghum landraces through multi-locus Genome-Wide Association Studies (ML-GWAS). 216 landraces, improved varieties, and check cultivars were obtained from the Ethiopian Biodiversity Institute and the National Sorghum Improvement Program for this study. The experiment was conducted over two cropping seasons, employing an α-lattice design for phenotyping key traits such as days to flowering, days to maturity, plant height, seed number per plant, grain yield, and thousand seed weight. A mixed linear model (MLM) was used to analyze the phenotypic data and estimate the genetic parameters including variances and the broad sense heritability. GBS with the ApeKI restriction enzyme provided 50,165 high-quality SNP markers. The six ML-GWAS models identified significant QTNs with a LOD score threshold value of ≥ 4.0. The analysis revealed major QTNs associated with traits across multiple chromosomes, supported by a stringent filtering criterion that ensured reliability. Co-localization with known QTLs was explored using the Sorghum QTL Atlas database and candidate genes within significant QTN regions, providing the genetic architecture influencing agronomic performance were identified via the Phytozome platform using the biomaRt package.

Result: Pearson correlation analysis revealed significant associations among most traits, with p-values less than 0.0001, except for grain yield per plant which showed lower correlations with other traits. Genetic variability analysis indicated that days to flowering exhibited high heritability (0.7) and genetic advance (19.6%) as percent of mean, suggesting strong genetic control, while grain yield displayed extremely low h2 (0.003). A total of 351,692 SNP markers were identified across 10 sorghum chromosomes from 216 Ethiopian sorghum landraces, and we have been refining this to 50,165 filtered SNPs. Manhattan plots indicated significant marker-trait associations (MTAs) across multiple chromosomes, particularly for days to flowering and plant height. Significant QTNs were associated with key traits including flowering time, plant height, and grain yield. ML-GWAS identified 176 QTNs with varying LOD scores and phenotypic effects. Multiple genes linked to these QTNs highlight the complexity of genetic interactions of studied traits with 36 unique and 12 major QTNs. Notable SNP markers were concentrated on chromosomes 1, 2, and 3, reinforcing the importance of these regions for breeding efforts. Candidate gene analysis revealed key genes regulating flowering time, stress response, and yield traits, which could serve as targets for genetic enhancement. In our study, key candidate genes have been successfully identified, these are regulating flowering time, maturity, and stress resilience. Genes such as Sobic.001G196700 and Sobic.002G183400 are identified as critical regulators of floral development. The stress-responsive gene Sobic.005G176100 (a mannose-6-phosphate isomerase), emphasizes the importance of resilience in sorghum cultivation under adverse conditions. Additionally, Sobic.003G324400 and Sobic.004G178300 are essential for regulating plant height and seed weight, making them valuable for yield enhancement breeding programs.

Conclusion: This study enhances our understanding of the genetic diversity of Ethiopian sorghum landraces, crucial for breeding programs. It identifies key QTNs and candidate genes associated with important agronomic traits, offering insights for marker-assisted and genomic-assisted breeding. The ML-GWAS models highlight the genetic complexity of flowering time and grain yield traits, emphasizing the need for targeted breeding efforts to maximize sorghum productivity.

背景:高粱是 7.5 亿多人的重要谷类作物,在全球排名第五。它有多种用途,包括粮食、饲料和生物燃料,在埃塞俄比亚至关重要,因为埃塞俄比亚的各个农业生态区具有丰富的遗传多样性:探索标记-性状关联(MTAs),利用多焦点 GWAS 模型鉴定埃塞俄比亚高粱陆地品系中与农艺性状和产量贡献性状相关的数量性状核苷酸(QTNs)和新的候选基因,以协助基因组辅助育种战略:本研究通过多焦点全基因组关联研究(ML-GWAS)探讨埃塞俄比亚高粱陆地品种农艺性状的遗传基础。本研究从埃塞俄比亚生物多样性研究所(Ethiopian Biodiversity Institute)和国家高粱改良计划(National Sorghum Improvement Program)获得了 216 个陆生高粱品种、改良品种和对照栽培品种。试验分两季进行,采用α-格子设计对开花天数、成熟天数、株高、单株种子数、谷物产量和千粒重等关键性状进行表型分析。采用混合线性模型(MLM)分析表型数据并估算遗传参数,包括方差和广义遗传率。使用 ApeKI 限制酶的 GBS 提供了 50,165 个高质量的 SNP 标记。六个 ML-GWAS 模型识别出了 LOD 分数阈值≥ 4.0 的重要 QTN。该分析揭示了与多条染色体上性状相关的主要 QTNs,严格的筛选标准确保了分析的可靠性。利用高粱 QTL Atlas 数据库探索了与已知 QTL 的共定位,并利用 biomaRt 软件包通过 Phytozome 平台确定了重要 QTN 区域内的候选基因,从而提供了影响农艺性状的遗传结构:皮尔逊相关性分析表明,除单株谷物产量与其他性状的相关性较低外,大多数性状之间都存在显著的相关性,且 p 值均小于 0.0001。遗传变异分析表明,开花天数表现出较高的遗传率(0.7)和遗传进展(19.6%)(占平均值的百分比),表明遗传控制能力很强,而谷物产量表现出极低的 h2(0.003)。我们从 216 个埃塞俄比亚高粱陆地品种的 10 条高粱染色体上共鉴定出 351,692 个 SNP 标记,并将其细化为 50,165 个筛选过的 SNP。曼哈顿图显示,多个染色体上的标记与性状之间存在显著的关联(MTAs),尤其是开花天数和株高。显著的 QTN 与开花时间、株高和谷物产量等关键性状相关。ML-GWAS 确定了 176 个 QTN,其 LOD 得分和表型效应各不相同。与这些 QTNs 相关的多个基因突显了所研究性状遗传相互作用的复杂性,其中有 36 个独特的 QTNs 和 12 个主要的 QTNs。显著的 SNP 标记集中在 1 号、2 号和 3 号染色体上,加强了这些区域对育种工作的重要性。候选基因分析揭示了调控花期、胁迫反应和产量性状的关键基因,这些基因可作为遗传改良的目标。在我们的研究中,成功鉴定出了关键候选基因,这些基因调控开花时间、成熟度和抗逆性。Sobic.001G196700和Sobic.002G183400等基因被确定为花发育的关键调控因子。胁迫响应基因 Sobic.005G176100(6-磷酸甘露糖异构酶)强调了高粱在不利条件下的抗逆性。此外,Sobic.003G324400 和 Sobic.004G178300 对调节植株高度和籽粒重量至关重要,因此它们对增产育种计划很有价值:本研究加深了我们对埃塞俄比亚高粱陆地品种遗传多样性的了解,这对育种计划至关重要。它确定了与重要农艺性状相关的关键 QTNs 和候选基因,为标记辅助育种和基因组辅助育种提供了启示。ML-GWAS 模型凸显了开花时间和谷物产量性状的遗传复杂性,强调了有针对性地开展育种工作以最大限度提高高粱产量的必要性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
BMC Genomics
BMC Genomics 生物-生物工程与应用微生物
CiteScore
7.40
自引率
4.50%
发文量
769
审稿时长
6.4 months
期刊介绍: BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics. BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
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