International Crops Research Institute for the Semi-Arid Tropics Hyderabad, India ; University School of Biotechnology, Guru Gobind Singh Indraprastha University Delhi, India.
International Crops Research Institute for the Semi-Arid Tropics Hyderabad, India ; Agronomy Department, University of Florida Gainesville, FL, USA.
Front Plant Sci. 2014 Jun 5;5:248. doi: 10.3389/fpls.2014.00248. eCollection 2014.
Chickpea is an important food legume crop for the semi-arid regions, however, its productivity is adversely affected by various biotic and abiotic stresses. Identification of candidate genes associated with abiotic stress response will help breeding efforts aiming to enhance its productivity. With this objective, 10 abiotic stress responsive candidate genes were selected on the basis of prior knowledge of this complex trait. These 10 genes were subjected to allele specific sequencing across a chickpea reference set comprising 300 genotypes including 211 genotypes of chickpea mini core collection. A total of 1.3 Mbp sequence data were generated. Multiple sequence alignment (MSA) revealed 79 SNPs and 41 indels in nine genes while the CAP2 gene was found to be conserved across all the genotypes. Among 10 candidate genes, the maximum number of SNPs (34) was observed in abscisic acid stress and ripening (ASR) gene including 22 transitions, 11 transversions and one tri-allelic SNP. Nucleotide diversity varied from 0.0004 to 0.0029 while polymorphism information content (PIC) values ranged from 0.01 (AKIN gene) to 0.43 (CAP2 promoter). Haplotype analysis revealed that alleles were represented by more than two haplotype blocks, except alleles of the CAP2 and sucrose synthase (SuSy) gene, where only one haplotype was identified. These genes can be used for association analysis and if validated, may be useful for enhancing abiotic stress, including drought tolerance, through molecular breeding.
鹰嘴豆是半干旱地区重要的食用豆科作物，但它的生产力受到各种生物和非生物胁迫的不利影响。鉴定与非生物胁迫反应相关的候选基因将有助于旨在提高其生产力的育种工作。为此，基于对该复杂性状的已有知识，选择了 10 个与非生物胁迫反应相关的候选基因。对包括 211 个鹰嘴豆核心小品种在内的 300 个基因型参考集的这 10 个基因进行了等位基因特异性测序。共产生了 1300 万 bp 的序列数据。多重序列比对（MSA）在九个基因中发现了 79 个 SNP 和 41 个插入缺失，而 CAP2 基因在所有基因型中都保守。在这 10 个候选基因中，在脱落酸胁迫和成熟（ASR）基因中观察到最多数量的 SNP（34 个），包括 22 个转换、11 个颠换和一个三等位 SNP。核苷酸多样性从 0.0004 到 0.0029 不等，而多态信息含量（PIC）值从 0.01（AKIN 基因）到 0.43（CAP2 启动子）不等。单倍型分析表明，除 CAP2 和蔗糖合酶（SuSy）基因的等位基因外，大多数等位基因都由两个以上的单倍型块表示，而这些基因只能识别一个单倍型。这些基因可用于关联分析，如果得到验证，可能有助于通过分子育种提高非生物胁迫，包括耐旱性。
