Genome wide association study and genomic prediction for stover quality traits in tropical maize (Zea mays L.)

Abstract

Maize is rapidly replacing traditionally cultivated dual purpose crops of South Asia, primarily due to the better economic remuneration. This has created an impetus for improving maize for both grain productivity and stover traits. Molecular techniques can largely assist breeders in determining approaches for effectively integrating stover trait improvement in their existing breeding pipeline. In the current study we identified a suite of potential genomic regions associated to the two major stover quality traits—in-vitro organic matter digestibility (IVOMD) and metabolizable energy (ME) through genome wide association study. However, considering the fact that the loci identified for these complex traits all had smaller effects and accounted only a small portion of phenotypic variation, the effectiveness of following a genomic selection approach for these traits was evaluated. The testing set consists of breeding lines recently developed within the program and the training set consists of a panel of lines from the working germplasm comprising the founder lines of the newly developed breeding lines and also an unrelated diversity set. The prediction accuracy as determined by the Pearson’s correlation coefficient between observed and predicted values of these breeding lines were high even at lower marker density (200 random SNPs), when the training and testing set were related. However, the accuracies were dismal, when there was no relationship between the training and the testing set.

Multi-trait and multi-environment genomic prediction for flowering traits in maize: a deep learning approach

“…Various studies have highlighted the potential of using GWAS and genomic selection approaches in enhancing crop breeding and developing improved maize varieties (e.g., Liu et al., 2021 ; Ma and Cao, 2021 ; Vinayan et al., 2021 ). For example, the study conducted by Zhou et al.…”

The brachytic2 mutation alone or its combination with the brown midrib3 mutation improves fiber digestibility in forage maize

“…Many quantitative trait loci and candidate genes have been identified to boost breeding efforts and accelerate the improvement of forage feeding value and biofuels (Barrière et al., 2009, 2016). Although many genomic regions have been highlighted as strong candidates for selection, their effects are rather small with multiple interactions, making the use of genome‐wide selection today the most effective approach to improve stover quality (Vinayan et al., 2021). Overall, our results demonstrate the potential of SSM, the mutation br2 alone or its combination with the bm3 mutation to produce silage with improved fiber digestibility.…”

Genomic and Transcriptomic Analyses Reveal Pathways and Genes Associated With Brittle Stalk Phenotype in Maize

“…Because of the fragile stalk strength, the brittle stalk trait in crops is clearly unfavorable for lodging resistance. However, reducing the content of cellulose and lignin can increase the digestibility of the stalk, which increases the feed value of crops, especially maize silage ( Wang et al, 2020 ; Vinayan et al, 2021 ). From this perspective, the brittle stalk trait in crops is favorable for the feed industry.…”