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An assessment of the performance of the logistic mixed model for analyzing binary traits in maize and sorghum diversity panels.

ABSTRACT: The logistic mixed model (LMM) is well-suited for the genome-wide association study (GWAS) of binary agronomic traits because it can include fixed and random effects that account for spurious associations. The recent implementation of a computationally efficient model fitting and testing approach now makes it practical to use the LMM to search for markers associated with such binary traits on a genome-wide scale. Therefore, the purpose of this work was to assess the applicability of the LMM for GWAS in crop diversity panels. We dichotomized three publicly available quantitative traits in a maize diversity panel and two quantitative traits in a sorghum diversity panel, and them performed a GWAS using both the LMM and the unified mixed linear model (MLM) on these dichotomized traits. Our results suggest that the LMM is capable of identifying statistically significant marker-trait associations in the same genomic regions highlighted in previous studies, and this ability is consistent across both diversity panels. We also show how subpopulation structure in the maize diversity panel can underscore the LMM's superior control for spurious associations compared to the unified MLM. These results suggest that the LMM is a viable model to use for the GWAS of binary traits in crop diversity panels and we therefore encourage its broader implementation in the agronomic research community.

SUBMITTER: Shenstone E

PROVIDER: S-EPMC6248992 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Sorghum, the fifth most important cereal crop, is a well-adapted cereal to arid/semi-arid regions. Sorghum is known for multiple end-uses as food, feed, fuel, forage, and as source of bioactive compounds that could be used for medical applications. Although the great improvement in the process of sorghum breeding, the average yield of this crop is still very low. Therefore, exploring the genetic diversity in sorghum accessions is a critical step for improving this crop. The main objective of the current work was to study the genetic variation existing in a Moroccan sorghum collection. Indeed, 10 sorghum ecotypes were characterized based on agromorphological descriptors. Both quantitative (25) and qualitative (7) traits revealed variability (p < 0.05) among the studied ecotypes. At the seedling stage, most of the ecotypes showed good to high vigor (70%). However, as the sorghum plants grow, the difference between genotypes become more apparent, especially at the generative phase. For instance, three different panicle shapes have been observed, erect (50%), semi-bent (30%), and bent (20%) with different degree of compactness (20% for loose, semi-compact, and compact panicles, and 30% for semi-loose panicles). In another part of this study, the phytochemical composition and antioxidant activities of the sorghum ecotypes have been determined. The results showed variable total phenolic contents, and total flavonoid contents ranging from 125.86 ± 1.36 to 314.91 ± 3.60 mg GAE/g dw and 114.0 ± 13.2 to 138.5 ± 10.8 (mg catechin equivalent/100 g, dw) respectively, with a differential antioxidant activities as well. These results indicate that for any crop breeding program, it is preferable to take into consideration both morphological and biochemical traits for a better selection of high yielding varieties with high added value compounds. Therefore, the implication of these results in the context of sorghum breeding activities could be a resourceful option for farmers.

Dataset Information

An assessment of the performance of the logistic mixed model for analyzing binary traits in maize and sorghum diversity panels.

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