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基于全基因组保守非编码微卫星（CNMS）标记的整合遗传基因组学用于鹰嘴豆种子重量的定量剖析

Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea.

作者信息

Bajaj Deepak, Saxena Maneesha S, Kujur Alice, Das Shouvik, Badoni Saurabh, Tripathi Shailesh, Upadhyaya Hari D, Gowda C L L, Sharma Shivali, Singh Sube, Tyagi Akhilesh K, Parida Swarup K

机构信息

National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.

Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India.

出版信息

J Exp Bot. 2015 Mar;66(5):1271-90. doi: 10.1093/jxb/eru478. Epub 2014 Dec 10.

DOI:10.1093/jxb/eru478
PMID:25504138
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4339591/
Abstract

Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5'-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea.

摘要

系统发育足迹分析从603个鹰嘴豆蛋白质编码基因的5'非翻译区和调控区（URR）中鉴定出666个全基因组旁系同源和直系同源保守非编码微卫星（CNMS）标记。分别携带CTRMCAMV35S和GAGA8BKN3调控元件的（CT）n和（GA）n CNMS在鹰嘴豆基因组中大量存在。具有强大扩增效率（94.7%）的定位基因CNMS标记在基因型间检测到较高的种内多态性潜力（37.6%），这意味着它们在鹰嘴豆育种和遗传分析中具有巨大的应用价值。通过整合遗传基因组学，选择了17个差异表达的CNMS标记相关基因，这些基因在不同基因型中表现出强烈的偏好性以及种子组织/发育阶段特异性表达，以缩小种子重量数量性状位点（QTL）/表达QTL（eQTL）潜在的基因靶点范围。转录谱分析与种子重量QTL/eQTL定位、分子单倍型分析和关联分析的整合，在控制鹰嘴豆种子重量顺式调控表达的含LOB结构域蛋白和KANADI蛋白编码转录因子基因中，鉴定出了潜在的分子标签（GAGA8BKN3和RAV1AAT调控元件以及等位基因/单倍型）。这突出了基于CNMS标记的整合遗传基因组学在鹰嘴豆复杂种子重量定量遗传剖析中的潜力。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/814d74967797/exbotj_eru478_f0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/de56397811fb/exbotj_eru478_f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/c077f0d07caa/exbotj_eru478_f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/653f8e35c5fd/exbotj_eru478_f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/d66ed5b02251/exbotj_eru478_f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/562c4ef1b182/exbotj_eru478_f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/2671afa0294e/exbotj_eru478_f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/fb5263effdab/exbotj_eru478_f0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/814d74967797/exbotj_eru478_f0008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/de56397811fb/exbotj_eru478_f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/c077f0d07caa/exbotj_eru478_f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/653f8e35c5fd/exbotj_eru478_f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/d66ed5b02251/exbotj_eru478_f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/562c4ef1b182/exbotj_eru478_f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/2671afa0294e/exbotj_eru478_f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/fb5263effdab/exbotj_eru478_f0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/ff15/4339591/814d74967797/exbotj_eru478_f0008.jpg

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