The genetics and physiology of seed dormancy, a crucial trait in common bean domestication

Abstract

Background Physical seed dormancy is an important trait in legume domestication. Although seed dormancy is beneficial in wild ecosystems, it is generally considered to be an undesirable trait in crops due to reduction in yield and / or quality. The physiological mechanism and underlying genetic factor(s) of seed dormancy is largely unknown in several legume species. Here we employed an integrative approach to understand the mechanisms controlling physical seed dormancy in common bean (Phaseolus vulgaris L.). Results Using an innovative CT scan imaging system, we were able to track water movements inside the seed coat. We found that water uptake initiates from the bean seed lens. Using a scanning electron microscopy (SEM) we further identified several micro-cracks on the lens surface of non-dormant bean genotypes. Bulked segregant analysis (BSA) was conducted on a bi-parental RIL (recombinant inbred line) population, segregating for seed dormancy. This analysis revealed that the seed water uptake is associated with a single major QTL on Pv03. The QTL region was fine-mapped to a 118 Kb interval possessing 11 genes. Coding sequence analysis of candidate genes revealed a 5-bp insertion in an ortholog of pectin acetylesterase 8 that causes a frame shift, loss-of-function mutation in non-dormant genotype. Gene expression analysis of the candidate genes in the seed coat of contrasting genotypes indicated 21-fold lower expression of pectin acetylesterase 8 in non-dormant genotype. An analysis of mutational polymorphism was conducted among wild and domesticated beans. Although all the wild beans possessed the functional allele of pectin acetylesterase 8, the majority (77%) of domesticated beans had the non-functional allele suggesting that this variant was under strong selection pressure through domestication. Conclusions In this study, we identified the physiological mechanism of physical seed dormancy and have identified a candidate allele causing variation in this trait. Our findings suggest that a 5-bp insertion in an ortholog of pectin acetylesterase 8 is likely a major causative mutation underlying the loss of seed dormancy during domestication. Although the results of current study provide strong evidences for the role of pectin acetylesterase 8 in seed dormancy, further confirmations seem necessary by employing transgenic approaches.

The Phaseolus vulgaris L. Yellow Bean Collection: genetic diversity and characterization for cooking time

“…All the significant SNPs for water uptake were novel when compared with previous studies using markers with known physical positions (Cichy et al 2015b;Berry et al 2020;Bassett et al 2021a, b;Diaz et al 2021;Soltani et al 2021). Several SNPs on Pv02 and Pv04 were significant in this study, and QTLs were detected on the same chromosomes in some previous studies with no physical position available (Pe ´rez-Vega et al 2010; Sandhu et al 2018).…”

Hotter chili peppers by hybridisation: heterosis and reciprocal effects

“…Enhanced seed germination is a key agronomic trait in cultivated species, as opposed to their highly dormant wild ancestors (Soltani et al, 2021). When C. annuum was used as the female parent, all crossing combinations with C. chinense yielded viable hybrids.…”

Seed germination and vigor: ensuring crop sustainability in a changing climate

“…Pre-harvest sprouting occurs when untimely rain before harvest causes seeds to germinate before being shed from the mother plant and is due to insufficient dormancy. Pre-harvest sprouting drastically reduces seed quality and longevity (Gualano et al 2014;Soltani et al 2021), where longevity is defined as seed viability after dry storage (Bewley et al 2013). Pre-harvest sprouting and its underlying genetics and regulation have been reviewed elsewhere (Rodríguez et al 2015;Vetch et al 2019).…”

“…QTLs associated with low-temperature stress in rapeseed have also been identified (Luo et al 2021). In common bean, a QTL analysis identified a locus associated with reduced physical seed dormancy in domesticated plants (Supplementary Table S1; Soltani et al 2021). Numerous QTLs for longevity in soybean (Dargahi et al 2014;Zhang et al 2019), lettuce (Schwember and Bradford 2010), and rapeseed (Wang et al 2018) provide a basis for breeding improved seed storage life of these crops.…”