鹰嘴豆（Cicer arietinum L.）耐旱性“QTL热点”区域候选基因的优先级排序。
Prioritization of candidate genes in "QTL-hotspot" region for drought tolerance in chickpea (Cicer arietinum L.).
作者信息
Kale Sandip M, Jaganathan Deepa, Ruperao Pradeep, Chen Charles, Punna Ramu, Kudapa Himabindu, Thudi Mahendar, Roorkiwal Manish, Katta Mohan Avsk, Doddamani Dadakhalandar, Garg Vanika, Kishor P B Kavi, Gaur Pooran M, Nguyen Henry T, Batley Jacqueline, Edwards David, Sutton Tim, Varshney Rajeev K
机构信息
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Center of Excellence in Genomics (CEG), Hyderabad, 502324, India.
Osmania University, Department of Genetics, Hyderabad, 500007, India.
出版信息
Sci Rep. 2015 Oct 19;5:15296. doi: 10.1038/srep15296.
A combination of two approaches, namely QTL analysis and gene enrichment analysis were used to identify candidate genes in the "QTL-hotspot" region for drought tolerance present on the Ca4 pseudomolecule in chickpea. In the first approach, a high-density bin map was developed using 53,223 single nucleotide polymorphisms (SNPs) identified in the recombinant inbred line (RIL) population of ICC 4958 (drought tolerant) and ICC 1882 (drought sensitive) cross. QTL analysis using recombination bins as markers along with the phenotyping data for 17 drought tolerance related traits obtained over 1-5 seasons and 1-5 locations split the "QTL-hotspot" region into two subregions namely "QTL-hotspot_a" (15 genes) and "QTL-hotspot_b" (11 genes). In the second approach, gene enrichment analysis using significant marker trait associations based on SNPs from the Ca4 pseudomolecule with the above mentioned phenotyping data, and the candidate genes from the refined "QTL-hotspot" region showed enrichment for 23 genes. Twelve genes were found common in both approaches. Functional validation using quantitative real-time PCR (qRT-PCR) indicated four promising candidate genes having functional implications on the effect of "QTL-hotspot" for drought tolerance in chickpea.
采用两种方法相结合，即QTL分析和基因富集分析，来鉴定鹰嘴豆Ca4假分子上耐旱“QTL热点”区域的候选基因。在第一种方法中，利用在ICC 4958（耐旱）和ICC 1882（干旱敏感）杂交的重组自交系（RIL）群体中鉴定出的53223个单核苷酸多态性（SNP）构建了高密度bin图谱。使用重组bin作为标记进行QTL分析，并结合在1至5个季节和1至5个地点获得的17个耐旱相关性状的表型数据，将“QTL热点”区域分为两个子区域，即“QTL热点_a”（15个基因）和“QTL热点_b”（11个基因）。在第二种方法中，基于Ca4假分子上的SNP与上述表型数据的显著标记-性状关联进行基因富集分析，来自精细“QTL热点”区域的候选基因显示有23个基因富集。在两种方法中发现有12个基因是共同的。使用定量实时PCR（qRT-PCR）进行功能验证表明，有四个有前景的候选基因对鹰嘴豆耐旱“QTL热点”的效应具有功能影响。
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