Zaidi P H, Seetharam K, Krishna Girish, Krishnamurthy L, Gajanan S, Babu Raman, Zerka M, Vinayan M T, Vivek B S
International Maize and Wheat Improvement Centre (CIMMYT), Asia regional office, Hyderabad, India.
International Crops research institute for semi-arid tropics (ICRISAT), Hyderabad, India.
PLoS One. 2016 Oct 21;11(10):e0164340. doi: 10.1371/journal.pone.0164340. eCollection 2016.
An association mapping panel, named as CIMMYT Asia association mapping (CAAM) panel, involving 396 diverse tropical maize lines were phenotyped for various structural and functional traits of roots under drought and well-watered conditions. The experiment was conducted during Kharif (summer-rainy) season of 2012 and 2013 in root phenotyping facility at CIMMYT-Hyderabad, India. The CAAM panel was genotyped to generate 955, 690 SNPs through GBS v2.7 using Illumina Hi-seq 2000/2500 at Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA. GWAS analysis was carried out using 331,390 SNPs filtered from the entire set of SNPs revealed a total of 50 and 67 SNPs significantly associated for root functional (transpiration efficiency, flowering period water use) and structural traits (rooting depth, root dry weight, root length, root volume, root surface area and root length density), respectively. In addition to this, 37 SNPs were identified for grain yield and shoot biomass under well-watered and drought stress. Though many SNPs were found to have significant association with the traits under study, SNPs that were common for more than one trait were discussed in detail. A total 18 SNPs were found to have common association with more than one trait, out of which 12 SNPs were found within or near the various gene functional regions. In this study we attempted to identify the trait specific maize lines based on the presence of favorable alleles for the SNPs associated with multiple traits. Two SNPs S3_128533512 and S7_151238865 were associated with transpiration efficiency, shoot biomass and grain yield under well-watered condition. Based on favorable allele for these SNPs seven inbred lines were identified. Similarly, four lines were identified for transpiration efficiency and shoot biomass under drought stress based on the presence of favorable allele for the common SNPs S1_211520521, S2_20017716, S3_57210184 and S7_130878458 and three lines were identified for flowering period water-use, transpiration efficiency, root dry weight and root volume based on the presence of favorable allele for the common SNPs S3_162065732 and S3_225760139.
一个名为国际玉米小麦改良中心亚洲关联分析（CAAM）群体的关联分析群体，由396个不同的热带玉米品系组成，在干旱和水分充足条件下对根的各种结构和功能性状进行了表型分析。该试验于2012年和2013年的雨季在印度海得拉巴的国际玉米小麦改良中心根系表型分析设施中进行。利用美国纽约州伊萨卡康奈尔大学基因组多样性研究所的Illumina Hi-seq 2000/2500，通过GBS v2.7对CAAM群体进行基因分型，以产生955,690个单核苷酸多态性（SNP）。使用从整个SNP集合中筛选出的331,390个SNP进行全基因组关联研究（GWAS）分析，结果显示分别有50个和67个SNP与根功能性状（蒸腾效率、花期水分利用）和结构性状（生根深度、根干重、根长、根体积、根表面积和根长密度）显著相关。除此之外，还鉴定出37个与水分充足和干旱胁迫下的籽粒产量和地上部生物量相关的SNP。尽管发现许多SNP与所研究的性状显著相关，但对多个性状共有的SNP进行了详细讨论。总共发现18个SNP与多个性状共有关联，其中12个SNP位于各种基因功能区域内或附近。在本研究中，我们试图根据与多个性状相关的SNP的有利等位基因的存在来鉴定性状特异的玉米品系。两个SNP，即S3_128533512和S7_151238865，与水分充足条件下的蒸腾效率、地上部生物量和籽粒产量相关。基于这些SNP的有利等位基因，鉴定出了7个自交系。同样，基于共有SNP S1_211520521、S2_20017716、S3_57210184和S7_130878458的有利等位基因的存在，鉴定出4个在干旱胁迫下与蒸腾效率和地上部生物量相关的品系；基于共有SNP S3_162065732和S3_225760139的有利等位基因的存在，鉴定出3个与花期水分利用、蒸腾效率、根干重和根体积相关的品系。
