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

• Published in: The plant genome 2024-12, Vol.17 (4), p.e20528-n/a
• Main Authors: Mohamedikbal, Shameela, Al‐Mamun, Hawlader A., Marsh, Jacob I., Upadhyaya, Shriprabha, Danilevicz, Monica F., Nguyen, Henry T., Valliyodan, Babu, Mahan, Adam, Batley, Jacqueline, Edwards, David
• Format: Article
• Language: English
• Subjects: Adaptability; Adaptation; Agricultural production; Association analysis; Bioinformatics; Chromosome 20; Chromosomes; Crop yield; Crops; Domestication; Flowering; Flowers & plants; Flowers - genetics; Flowers - physiology; Genetic control; Genetic diversity; Genomes; Genomic analysis; Germplasm; Glycine max - genetics; Glycine max - physiology; Haplotypes; Histones; Influence; Legumes; Linkage analysis; Original; Phenotypic variations; Plant breeding; Polymorphism; Quantitative Trait Loci; Rice; Seeds; Sorghum; Soybeans; Subpopulations
• ISSN: 1940-3372; 1940-3372
• DOI: 10.1002/tpg2.20528

The timing of flowering in soybean [Glycine max (L.) Merr.], a key legume crop, is influenced by many factors, including daylight length or photoperiodic sensitivity, that affect 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 915 domesticated and wild‐type individuals. The association analysis identified eight significant loci on seven chromosomes. 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 thaliana (L.) Heynh. 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. Core Ideas Flowering in soybean is influenced by many factors, including photoperiod, that affect yield and latitude adaptability. We conducted association tests and local haplotyping to identify genomic regions influencing flowering using 915 soybean lines. We found distinct haplotype structures potentially influencing flowering on chromosomes 6 and 20. These findings support future functional validation of haplotype‐based alleles for marker‐assisted breeding and genomic selection. Plain Language 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 wildtype soybean