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ARS Home » Midwest Area » Urbana, Illinois » Soybean/maize Germplasm, Pathology, and Genetics Research » Research » Publications at this Location » Publication #417069
Research Project: Maintenance, Characterization, Evaluation, and Enhancement of Genetic Resources in the National Soybean Germplasm Collection

Location: Soybean/maize Germplasm, Pathology, and Genetics Research

Title: Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean

Author
item MOHAMEDIKBAL, SHAMELLA - The University Of Western Australia
item AL-MAMUN, HAWLADER - The University Of Western Australia
item MARSH, JACOB - University Of North Carolina
item UPADHYAYA, SHRIPRABHA - The University Of Western Australia
item DANILEVICZ, MONICA - The University Of Western Australia
item NGUYEN, HENRY - University Of Missouri
item VALLIYODAN, BABU - Lincoln University Of Missouri
item Mahan, Adam
item BATLEY, JACQUELINE - The University Of Western Australia
item EDWARDS, DAVID - The University Of Western Australia

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/13/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: This study focuses on understanding the genetic factors that cause some soybean varieties to flower early while others flower later, a trait that influences their adaptation to different latitudes. We investigated the patterns of DNA sequence variation in cultivated and wild type soybean using advanced bioinformatics tools, focusing on combinations of genetic variation that are inherited together. Our results show the presence of distinct DNA sequences in wild and cultivated soybeans, and their influence on flowering time. Understanding these genetic variations helps in breeding varieties that can be grown in different latitudes with optimal flowering time.

Technical Abstract: The timing of flowering in soybean, a key legume crop, is influenced by many factors including daylight length or photoperiodic sensitivity, that affects crop yield, productivity, and geographical adaptation. Despite its importance, a comprehensive understanding of the local linkage landscape and allelic diversity within regions of the genome influencing flowering and contributing to phenotypic variation in subpopulations has been limited. This study addresses these gaps by conducting an in-depth trait-association and linkage analysis coupled with local haplotyping using advanced bioinformatics tools including crosshap, to characterize genomic variation using a pangenome dataset representing 916 domesticated and wild type individuals. The association analysis identified eight significant loci, with co-localisation of days to flower quantitative trait loci with other yield-related traits, suggesting potential pleiotropic effects. Moving beyond traditional association analysis, local haplotyping of targeted regions on chromosomes 6 and 20 identified distinct haplotype structures, variation patterns and genomic candidates influencing flowering in subpopulations. These results suggest the action of a network of genomic candidates influencing flowering time, and an untapped reservoir of genomic variation for this trait in wild germplasm. Notably, GlymaLee.20G147200 on chromosome 20 was identified as a candidate gene that may cause delayed flowering in soybean, potentially through histone modifications of floral repressor loci as seen in Arabidopsis. These findings support future functional validation of haplotype-based alleles for marker-assisted breeding and genomic selection, to enhance latitude adaptability of soybean without compromising yield.