Abstract
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.
Highlights
In Asian tropics maize is largely grown as rain-fed crop, which is prone to face vagaries of monsoon rains associated with an array of abiotic and biotic constraints
Broad-sense heritability for all the traits was high across moisture regimes (h >0.7), except anthesis silking interval (ASI) under wellwatered condition (h = 0.41)
Grain yield under well-watered conditions based on the favorable allele for two SNPs S3_1285 33512 and S7_151238865, 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
Summary
In Asian tropics maize is largely (about 80%) grown as rain-fed crop, which is prone to face vagaries of monsoon rains associated with an array of abiotic and biotic constraints. Erratic/ un-even distribution patterns of monsoon rain occasionally causes drought at different crop growth stage(s), which is identified as a factor responsible for year-to-year fluctuation in production of rainfed maize in Asian tropics[1]. One of the strategies for improving yields in drought-prone rainfed system, when water availability in the root zone constrains crop growth, is to develop deeper and more profuse rooting system to access water from soil profile [7,8] and use the available water more efficiently (increasing water productivity) by increasing the water use efficiency [9,10]. Understanding how roots respond (or adjust) to stress conditions, and support adaptation to the stress is crucial for developing stress-resilient genotypes and there are several studies reported significant association between root traits and crop performance [11,12]. Keeping in view complexity in direct studies on root traits [17], the alternative for studying the available genotypic variability of such complex traits is to identify superior alleles through genome-wide association studies (GWAS), and use in forward breeding through marker-assisted introgression of desirable genomic regions in elite genetic background
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