An efficient and cost-effective approach for genic microsatellite marker-based large-scale trait association mapping: identification of candidate genes for seed weight in chickpea
An efficient and cost-effective approach for genic microsatellite marker-based large-scale trait association mapping: identification of candidate genes for seed weight in chickpea
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DOI：
10.1007/s11032-014-0033-3
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发表时间：
2014-06-01
影响因子：
3.1
通讯作者：
Parida, Swarup K.
中科院分区：
文献类型：
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作者：
Kujur, Alice;Bajaj, Deepak;Parida, Swarup K.
大规模的验证和高通量基因分型的许多信息基因微卫星标记的关联作图，以确定候选基因的复杂的数量性状在鹰嘴豆。然而，由于鹰嘴豆的遗传多态性低，在用于性状关联作图的个体基因型/整体关联组中筛选和基因分型此类信息标记涉及资源、时间和劳动力方面的巨大成本。我们已经开发了一种节省时间和成本效益的池为基础的性状关联映射方法相结合的汇集DNA分析（616个基因微卫星标记）和个体基因型（大结构关联面板）基因分型。使用这种方法，我们已经确定了7个种子重量相关的转录因子基因衍生的微卫星标记（与次要等位基因频率> 15%）在德西和卡布里鹰嘴豆。这五个转录因子的强标记等位基因效应随着种子重量的增加而在对比的德西和卡布里基因型中是明显的。利用241个微卫星标记进行双亲连锁作图，发现了9个与3个主要数量性状位点连锁的微卫星标记（解释23.5- 34.7%的总表型变异）（CaqSW1.1：73.5- 74.5cM和CaqSW1.2：79.3- 81.3cM）和2（CaqSW2.1：65.7- 67.5cM）控制鹰嘴豆的百粒重。基于池的性状关联作图与差异表达谱分析、传统双亲连锁作图和基于高分辨率微卫星-单核苷酸多态性标记的单体型分析/连锁不平衡作图相结合，确定了4个控制德西和卡布里鹰嘴豆种子重量的转录因子基因（DUF 3594、bZIP、DUF 1635和SBP）。在我们的研究中实施的策略可用于大规模的性状关联映射的候选基因的快速识别和在包括鹰嘴豆的作物物种的农业重要性的性状的功能标记的发展。
The large-scale validation and high-throughput genotyping of numerous informative genic microsatellite markers are required for association mapping to identify candidate genes for complex quantitative traits in chickpea. However, the screening and genotyping of such informative markers in individual genotypes/whole association panels for trait association mapping involves massive costs in terms of resources, time and labour due to low genetic polymorphism in chickpea. We have developed an alternative time-saving and cost-effective pool-based trait association mapping approach by combining pooled DNA analysis (with 616 genic microsatellite markers) and individual genotype (large structured association panel) genotyping. Using this approach we have identified seven seed weight-associated transcription factor gene-derived microsatellite markers (with minor allele frequency > 15 %) in desi and kabuli chickpea. Strong marker allele effects of these five transcription factors with increasing seed weight in the contrasting desi and kabuli genotypes were evident. Bi-parental linkage mapping using 241 of the informative gene-based microsatellite markers resulted in the identification and mapping of nine such markers linked with three major quantitative trait loci (explaining a total phenotypic variance of 23.5-34.7 %) on chromosomes 1 (CaqSW1.1: 73.5-74.5 cM and CaqSW1.2: 79.3-81.3 cM) and 2 (CaqSW2.1: 65.7-67.5 cM) controlling 100-seed weight in chickpea. The integration of pool-based trait association mapping with differential expression profiling, traditional bi-parental linkage mapping and high-resolution microsatellite-single nucleotide polymorphism marker-based haplotyping/linkage disequilibrium mapping delineated four transcription factor genes (DUF3594, bZIP, DUF1635 and SBP) controlling seed weight in desi and kabuli chickpea. The strategies implemented in our study can be used in large-scale trait association mapping for the rapid identification of candidate genes and in the development of functional markers for traits of agricultural importance in crop species including chickpea.