Upadhyaya Hari D, Bajaj Deepak, Srivastava Rishi, Daware Anurag, Basu Udita, Tripathi Shailesh, Bharadwaj Chellapilla, Tyagi Akhilesh K, Parida Swarup K
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.
Funct Integr Genomics. 2017 Nov;17(6):711-723. doi: 10.1007/s10142-017-0566-8. Epub 2017 Jun 9.
A combinatorial genomics-assisted breeding strategy encompassing association analysis, genetic mapping and expression profiling is found most promising for quantitative dissection of complex traits in crop plants. The present study employed GWAS (genome-wide association study) using 24,405 SNPs (single nucleotide polymorphisms) obtained with genotyping-by-sequencing (GBS) of 92 sequenced desi and kabuli accessions of chickpea. This identified eight significant genomic loci associated with erect (E)/semi-erect (SE) vs. spreading (S)/semi-spreading (SS)/prostrate (P) plant growth habit (PGH) trait differentiation regardless of diverse desi and kabuli genetic backgrounds of chickpea. These associated SNPs in combination explained 23.8% phenotypic variation for PGH in chickpea. Five PGH-associated genes were validated successfully in E/SE and SS/S/P PGH-bearing parental accessions and homozygous individuals of three intra- and interspecific RIL (recombinant inbred line) mapping populations as well as 12 contrasting desi and kabuli chickpea germplasm accessions by selective genotyping through Sequenom MassARRAY. The shoot apical, inflorescence and floral meristems-specific expression, including upregulation (seven-fold) of five PGH-associated genes especially in germplasm accessions and homozygous RIL mapping individuals contrasting with E/SE PGH traits was apparent. Collectively, this integrated genomic strategy delineated diverse non-synonymous SNPs from five candidate genes with strong allelic effects on PGH trait variation in chickpea. Of these, two vernalization-responsive non-synonymous SNP alleles carrying SNF2 protein-coding gene and B3 transcription factor associated with PGH traits were found to be the most promising in chickpea. The SNP allelic variants associated with E/SE/SS/S PGH trait differentiation were exclusively present in all cultivated desi and kabuli chickpea accessions while wild species/accessions belonging to primary, secondary and tertiary gene pools mostly contained prostrate PGH-associated SNP alleles. This indicates strong adaptive natural/artificial selection pressure (Tajima's D 3.15 to 4.57) on PGH-associated target genomic loci during chickpea domestication. These vital leads thus have potential to decipher complex transcriptional regulatory gene function of PGH trait differentiation and for understanding the selective sweep-based PGH trait evolution and domestication pattern in cultivated and wild chickpea accessions adapted to diverse agroclimatic conditions. Collectively, the essential inputs generated will be of profound use in marker-assisted genetic enhancement to develop cultivars with desirable plant architecture of erect growth habit types in chickpea.
一种包括关联分析、遗传图谱构建和表达谱分析的组合基因组学辅助育种策略，被发现对于作物复杂性状的定量剖析最具前景。本研究采用全基因组关联研究（GWAS），利用通过对92份测序的鹰嘴豆迪西和卡布利种质进行测序基因分型（GBS）获得的24,405个单核苷酸多态性（SNP）。这确定了8个与鹰嘴豆直立（E）/半直立（SE）与展开（S）/半展开（SS）/匍匐（P）植株生长习性（PGH）性状分化相关的显著基因组位点，而不考虑鹰嘴豆不同的迪西和卡布利遗传背景。这些相关的SNP共同解释了鹰嘴豆PGH 23.8%的表型变异。通过Sequenom MassARRAY进行选择性基因分型，在具有E/SE和SS/S/P PGH的亲本种质以及三个种内和种间重组自交系（RIL）作图群体的纯合个体以及12个对比的迪西和卡布利鹰嘴豆种质中成功验证了5个与PGH相关的基因。芽顶端、花序和花分生组织特异性表达明显，包括5个与PGH相关的基因上调（7倍），特别是在与E/SE PGH性状对比的种质和纯合RIL作图个体中。总体而言，这种整合的基因组策略从5个候选基因中描绘出了对鹰嘴豆PGH性状变异具有强烈等位基因效应的不同非同义SNP。其中，两个携带与PGH性状相关的SNF2蛋白编码基因和B3转录因子的春化响应非同义SNP等位基因在鹰嘴豆中被发现最具前景。与E/SE/SS/S PGH性状分化相关的SNP等位变异仅存在于所有栽培的迪西和卡布利鹰嘴豆种质中，而属于初级、次级和三级基因库的野生种/种质大多含有与匍匐PGH相关的SNP等位基因。这表明在鹰嘴豆驯化过程中，PGH相关目标基因组位点受到强烈的适应性自然/人工选择压力（Tajima's D为3.15至4.57）。因此，这些重要线索有可能破译PGH性状分化的复杂转录调控基因功能，并有助于理解适应不同农业气候条件的栽培和野生鹰嘴豆种质中基于选择性清除的PGH性状进化和驯化模式。总体而言，所产生的重要信息将在标记辅助遗传改良中具有深远用途，以培育具有理想直立生长习性类型植株结构的鹰嘴豆品种。
