International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India.
National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
Plant Mol Biol. 2015 Nov;89(4-5):403-20. doi: 10.1007/s11103-015-0377-z. Epub 2015 Sep 22.
A combinatorial approach of candidate gene-based association analysis and genome-wide association study (GWAS) integrated with QTL mapping, differential gene expression profiling and molecular haplotyping was deployed in the present study for quantitative dissection of complex flowering time trait in chickpea. Candidate gene-based association mapping in a flowering time association panel (92 diverse desi and kabuli accessions) was performed by employing the genotyping information of 5724 SNPs discovered from 82 known flowering chickpea gene orthologs of Arabidopsis and legumes as well as 832 gene-encoding transcripts that are differentially expressed during flower development in chickpea. GWAS using both genome-wide GBS- and candidate gene-based genotyping data of 30,129 SNPs in a structured population of 92 sequenced accessions (with 200-250 kb LD decay) detected eight maximum effect genomic SNP loci (genes) associated (34% combined PVE) with flowering time. Six flowering time-associated major genomic loci harbouring five robust QTLs mapped on a high-resolution intra-specific genetic linkage map were validated (11.6-27.3% PVE at 5.4-11.7 LOD) further by traditional QTL mapping. The flower-specific expression, including differential up- and down-regulation (>three folds) of eight flowering time-associated genes (including six genes validated by QTL mapping) especially in early flowering than late flowering contrasting chickpea accessions/mapping individuals during flower development was evident. The gene haplotype-based LD mapping discovered diverse novel natural allelic variants and haplotypes in eight genes with high trait association potential (41% combined PVE) for flowering time differentiation in cultivated and wild chickpea. Taken together, eight potential known/candidate flowering time-regulating genes [efl1 (early flowering 1), FLD (Flowering locus D), GI (GIGANTEA), Myb (Myeloblastosis), SFH3 (SEC14-like 3), bZIP (basic-leucine zipper), bHLH (basic helix-loop-helix) and SBP (SQUAMOSA promoter binding protein)], including novel markers, QTLs, alleles and haplotypes delineated by aforesaid genome-wide integrated approach have potential for marker-assisted genetic improvement and unravelling the domestication pattern of flowering time in chickpea.
本研究采用候选基因关联分析和全基因组关联研究（GWAS）相结合的组合方法，结合 QTL 作图、差异基因表达谱分析和分子单体型分析，对鹰嘴豆复杂开花时间性状进行定量剖析。在一个开花时间关联面板（92 个不同的 Desi 和 Kabuli 品种）中进行了基于候选基因的关联作图，该面板使用了从 82 个已知的拟南芥和豆类开花鹰嘴豆基因直系同源物以及 832 个在鹰嘴豆花发育过程中差异表达的基因编码转录本中发现的 5724 个 SNP 的基因型信息。在一个由 92 个已测序品种（200-250 kb LD 衰减）组成的结构群体中，使用全基因组 GBS 和基于候选基因的 30129 个 SNP 的 GWAS 检测到与开花时间相关的 8 个最大效应基因组 SNP 位点（基因）（34%的联合 PVE）。六个与开花时间相关的主要基因组位点包含五个稳健的 QTL，这些 QTL映射在一个高分辨率的种内遗传连锁图谱上，通过传统的 QTL 作图进一步验证（5.4-11.7 LOD 时的 11.6-27.3% PVE）。在花发育过程中，特别是在早开花和晚开花的鹰嘴豆品种/作图个体中，发现了与 8 个开花时间相关基因（包括通过 QTL 作图验证的 6 个基因）的特异性表达，包括差异上调和下调（>三倍）。基于基因单体型的 LD 作图发现了 8 个具有高性状关联潜力（41%的联合 PVE）的基因中的多种新型天然等位基因变异体和单体型，这些基因与栽培和野生鹰嘴豆的开花时间分化有关。综上所述，八个潜在的已知/候选开花时间调节基因 [efl1（早期开花 1）、FLD（开花 locus D）、GI（GIGANTEA）、Myb（Myeloblastosis）、SFH3（SEC14-like 3）、bZIP（basic-leucine zipper）、bHLH（basic helix-loop-helix）和 SBP（SQUAMOSA promoter binding protein）]，包括通过上述全基因组综合方法划定的新型标记、QTL、等位基因和单体型，具有辅助遗传改良和揭示鹰嘴豆花时间驯化模式的潜力。
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