Genome-wide association studies dissect the genetic architecture of seed shape and size in common bean.

Abstract

Seed weight and size are important yield components. Thus, selecting for large seeds has been a key objective in crop domestication and breeding. In common bean, seed shape is also important since it influences industrial processing and plays a vital role in determining the choices of consumers and farmers. In this study, we performed genome-wide association studies on a core collection of common bean accessions to dissect the genetic architecture and identify genomic regions associated with seed morphological traits related to weight, size, and shape. Phenotypic data were collected by high-throughput image-based approaches, and utilized to test associations with 10,362 single-nucleotide polymorphism markers using multilocus mixed models. We searched within genome-associated regions for candidate genes putatively involved in seed phenotypic variation. The collection exhibited high variability for the entire set of seed traits, and the Andean gene pool was found to produce larger, heavier seeds than the Mesoamerican gene pool. Strong pairwise correlations were verified for most seed traits. Genome-wide association studies identified marker-trait associations accounting for a considerable amount of phenotypic variation in length, width, projected area, perimeter, and circularity in 4 distinct genomic regions. Promising candidate genes were identified, e.g. those encoding an AT-hook motif nuclear-localized protein 8, type 2C protein phosphatases, and a protein Mei2-like 4 isoform, known to be associated with seed size and weight regulation. Moreover, the genes that were pinpointed are also good candidates for functional analysis to validate their influence on seed shape and size in common bean and other related crops.

Plant phenotyping relevance

高スループット画像法による種子形状・サイズ形質の取得が明示され、GWASのための中心的な表現型データ取得手法として扱われているため。

Code and data availability

The paper's phenotypic dataset (Supplementary Files 1–3) and analysis source code (Supplementary File 4) are described as available, but only via 'Supplemental material is available at G3 online', and no G3 supplementary URL appears in allowed_urls. The BioProject PRJNA336556 link is a GBS sequencing deposit (molecular

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