Anti-MBP monoclonal antibody, clone 8E3

Gene flow has tremendous importance for local adaptation, by influencing the fate of de novo mutations, maintaining standing genetic variation and driving adaptive introgression. Furthermore, structural variation as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding of the evolutionary mechanisms impending or favouring local adaptation in the presence of gene flow is still limited to a restricted number of study systems. In this study, we examined how demographic history, shared ancestral polymorphism, arid gene flow among glacial lineages contribute to local adaptation to sea conditions in a marine fish, the capelin (Mallotus villosus). We first assembled a 490-Mbp draft genome of M. villosus to map our RAD sequence reads. Then, we used a large data set of genome-wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,310 individuals collected from 31 spawning sites in the northwest Atlantic. We reconstructed the history of divergence among three glacial lineages and showed that they probably diverged from 3.8 to 1.8 million years ago and experienced secondary contacts. Within each lineage, our analyses provided evidence for large N e and high gene flow among spawning sites. Within the Northwest Atlantic lineage, we detected a polymorphic chromosomal rearrangement leading to the occurrence of three haplogroups. Genotype-environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Our study also suggests that both shared polymorphisms among lineages, resulting from standing genetic variation or introgression, and chromosomal rearrangements may contribute to local adaptation in the presence of high gene flow.

Key message Several QTL governing color retention in processed black beans were identified by traditional and novel phenotyping methods applied to two black bean mapping populations. When black beans are hydrothermally processed prior to consumption, water-soluble anthocyanins are released from the seed coat, resulting in an undesirable faded brown color in the cooked product. The aim of this research was to develop mapping populations with different genetic sources of color retention in order to identify regions of the bean genome associated with canning quality traits. Two half-sibling black bean recombinant inbred line (RIL) populations segregating for post-processing color retention were developed. These RIL populations were phenotyped for canning quality traits over two years and genotyped using the BARCBean6k_3 BeadChip. In addition to traditional phenotyping by trained panelists, cooked beans were also phenotyped using a novel digital image analysis pipeline. Measurements of post-processing seed coat color from both phenotyping methods were compared, and the digital image analysis was shown to outperform the trained panelists. Quantitative trait loci (QTL) for post-processing color retention were detected on six chromosomes, with QTL on Pv08 and Pv11 consistently detected across phenotyping methods, populations, and years. Color retention QTL on Pv08 explained up to 32% of phenotypic variation but were significant over a large physical interval due to low SNP marker coverage. However, color retention QTL on Pv11 also explained a substantial amount of phenotypic variation (r(2) approximate to 25%) and mapped to a small genomic region near 52.5 Mbp. The QTL and methods described in this study will be useful for dry bean breeders and food scientists to produce high quality black beans that meet consumer needs.