Chandana B S, Mahto Rohit Kumar, Singh Rajesh Kumar, Bhandari Aditi, Tandon Gitanjali, Singh K K, Kushwah Sunita, Lavanya Gera Roopa, Iquebal Mir Asif, Jain Neelu, Kudapa Himabindu, Upadhyaya H D, Hamwieh Aladdin, Kumar Rajendra
Division of Genetics, Indian Agricultural Statistics Research Institute (ICAR)-Indian Agricultural Research Institute, New Delhi, India.
School of Biotechnology, Institute of Science, Banaras Hindu University (BHU), Varanasi, India.
Front Plant Sci. 2024 Oct 15;15:1395938. doi: 10.3389/fpls.2024.1395938. eCollection 2024.
The chickpea (Cicer arietinum L.) is well-known for having climate resilience and atmospheric nitrogen fixation ability. Global demand for nitrogenous fertilizer is predicted to increase by 1.4% annually, and the loss of billions of dollars in farm profit has drawn attention to the need for alternative sources of nitrogen. The ability of chickpea to obtain sufficient nitrogen via its symbiotic relationship with is of critical importance in determining the growth and production of chickpea.
To support findings on nodule formation in chickpea and to map the genomic regions for nodulation, an association panel consisting of 271 genotypes, selected from the global chickpea germplasm including four checks at four locations, was evaluated, and data were recorded for nodulation and 12 yield-related traits. A genome-wide association study (GWAS) was conducted using phenotypic data and genotypic data was extracted from whole-genome resequencing data of chickpea by creating a hap map file consisting of 602,344 single-nucleotide polymorphisms (SNPs) in the working set with best-fit models of association mapping.
The GWAS panel was found to be structured with sufficient diversity among the genotypes. Linkage disequilibrium (LD) analysis showed an LD decay value of 37.3 MB, indicating that SNPs within this distance behave as inheritance blocks. A total of 450 and 632 stringent marker-trait associations (MTAs) were identified from the BLINK and FarmCPU models, respectively, for all the traits under study. The 75 novel MTAs identified for nodulation traits were found to be stable. SNP annotations of associated markers were found to be related to various genes including a few auxins encoding as well as nod factor transporter genes. The identified significant MTAs, candidate genes, and associated markers have the potential for use in marker-assisted selection for developing high-nodulation cultivars after validation in the breeding populations.
鹰嘴豆（Cicer arietinum L.）以具有气候适应能力和大气固氮能力而闻名。预计全球对氮肥的需求将以每年1.4%的速度增长，农场利润损失数十亿美元已引起人们对替代氮源需求的关注。鹰嘴豆通过与根瘤菌的共生关系获取足够氮的能力对于决定鹰嘴豆的生长和产量至关重要。
为了支持关于鹰嘴豆根瘤形成的研究结果并绘制结瘤的基因组区域，对一个由271个基因型组成的关联群体进行了评估，这些基因型选自全球鹰嘴豆种质，包括四个对照品种，在四个地点种植，并记录了结瘤和12个产量相关性状的数据。使用表型数据进行全基因组关联研究（GWAS），并通过创建一个包含602,344个单核苷酸多态性（SNP）的单倍型图谱文件，从鹰嘴豆全基因组重测序数据中提取基因型数据，采用最佳拟合的关联图谱模型。
发现GWAS群体在基因型之间具有足够的多样性结构。连锁不平衡（LD）分析显示LD衰减值为37.3兆碱基对，表明在此距离内的SNP表现为遗传块。分别从BLINK和FarmCPU模型中为所有研究性状鉴定出总共450个和632个严格的标记-性状关联（MTA）。发现为结瘤性状鉴定出的75个新MTA是稳定的。发现相关标记的SNP注释与各种基因有关，包括一些编码生长素的基因以及结瘤因子转运蛋白基因
