Genome Wide Association Study for Drought, Aflatoxin Resistance, and Important Agronomic Traits of Maize Hybrids in the Sub-Tropics

Abstract

The primary maize (Zea mays L.) production areas are in temperate regions throughout the world and this is where most maize breeding is focused. Important but lower yielding maize growing regions such as the sub-tropics experience unique challenges, the greatest of which are drought stress and aflatoxin contamination. Here we used a diversity panel consisting of 346 maize inbred lines originating in temperate, sub-tropical and tropical areas testcrossed to stiff-stalk line Tx714 to investigate these traits. Testcross hybrids were evaluated under irrigated and non-irrigated trials for yield, plant height, ear height, days to anthesis, days to silking and other agronomic traits. Irrigated trials were also inoculated with Aspergillus flavus and evaluated for aflatoxin content. Diverse maize testcrosses out-yielded commercial checks in most trials, which indicated the potential for genetic diversity to improve sub-tropical breeding programs. To identify genomic regions associated with yield, aflatoxin resistance and other important agronomic traits, a genome wide association analysis was performed. Using 60,000 SNPs, this study found 10 quantitative trait variants for grain yield, plant and ear height, and flowering time after stringent multiple test corrections, and after fitting different models. Three of these variants explained 5–10% of the variation in grain yield under both water conditions. Multiple identified SNPs co-localized with previously reported QTL, which narrows the possible location of causal polymorphisms. Novel significant SNPs were also identified. This study demonstrated the potential to use genome wide association studies to identify major variants of quantitative and complex traits such as yield under drought that are still segregating between elite inbred lines.

Development of a multiple-hybrid population for genome-wide association studies: theoretical consideration and genetic mapping of flowering traits in maize

“…Testing of multiple hybrids across diverse environments has been also used in genetic study. For example, testcrosses between Tx714 and 346 diverse inbreds evaluated under well watered and non-irrigated trials showed high genetic variance, and for 10 quantitative trait variants for agronomic traits as revealed by 60,000 SNPs, three of them explained 5–10% of phenotypic variation in grain yield under both water conditions44. In our research, hybrids from the MHP showed a high level of genetic and phenotypic variation across different environments (data not shown).…”

Four‐Parent Maize (FPM) Population: Development and Phenotypic Characterization

“…The relatively low levels of residual variation for all traits were encouraging, given that single replications among experimental entries (in a single environment) can lead to unaccounted sources of variation. Accounting for field variation with blocking or other methods is always useful to test but often carries increased importance for yield trials in Texas where furrow irrigation is used, as it was here (Barrero et al, 2015). Across all five environments (Table 3), field variation (block) was significant, but the proportion of the total variation (2.4-6.6%) coming from this effect was low.…”

A genome‐wide association study for partial resistance to southern corn rust in tropical maize

“…GWAS generally have better mapping resolution than biparental mapping and have become more widely available to plant researchers (Gao, Kathryn Turner, Chao, Kolmer, & Anderson, ). In maize, GWAS have been used successfully to study agronomic traits (Farfan et al, ; Tian et al, ), quality traits (Owens et al, ; Suwarno, Pixley, Palacios‐Rojas, Kaeppler, & Babu, ), pest resistance (Samayoa, Malvar, Olukolu, Holland, & Butrón, ) and disease resistance (Coan et al, ; Gowda et al, ; Zila et al, ).…”