Yujiao Liu

A comprehensive study of the genome and genetics of superior germplasms is fundamental for crop improvement. As a widely adapted protein crop with high yield potential, the improvement in breeding and development of the seeds industry of faba bean have been greatly hindered by its giant genome size and high outcrossing rate. To fully explore the genomic diversity and genetic basis of important agronomic traits, we first generate a de novo genome assembly and perform annotation of a special short-wing petal faba bean germplasm (VF8137) exhibiting a low outcrossing rate. Comparative genome and pan-genome analyses reveal the genome evolution characteristics and unique pan-genes among the three different faba bean genomes. In addition, the genome diversity of 558 accessions of faba bean germplasm reveals three distinct genetic groups and remarkable genetic differences between the southern and northern germplasms. Genome-wide association analysis identifies several candidate genes associated with adaptation- and yield-related traits. We also identify one candidate gene related to short-wing petals by combining quantitative trait locus mapping and bulked segregant analysis. We further elucidate its function through multiple lines of evidence from functional annotation, sequence variation, expression differences, and protein structure variation. Our study provides new insights into the genome evolution of Leguminosae and the genomic diversity of faba bean. It offers valuable genomic and genetic resources for breeding and improvement of faba bean.

Cotyledon color is one of the important indices for identifying faba bean variety purity and measuring processing quality. Therefore, an in-depth study of the genetic mechanism of cotyledon color is vital for promoting faba bean industry development. We used the yellow cotyledon variety Qingcan 16 and the green cotyledon variety Qingcan 17 as parent plants to construct hybrid combinations. F₁-, F₂-, BC₁F₁-, and BC₂F₁-generation single-plant cotyledon colors were counted to clarify cotyledon color inheritance. F₂-generation individuals were genotyped using ddRAD-Seq to construct a genetic linkage map and identify QTLs for cotyledon color. Green cotyledons were controlled by one pair of recessive nuclear genes. Using the screened 1991 SNP markers, a high-density linkage map was constructed, with a coverage length of 1476.95 cM and an average map distance of 0.96 cM. The green cotyledon trait was located using WinQTL Cart, and a vfGC candidate interval explaining 34.30 to 49.40% of the phenotypic variation was identified at LG02 (101.952 cM to 115.493 cM) and at LOD = 16.0, corresponding to chr1L 1,077,051,302 bp to 1,636,400,339 bp (559.35 Mb). The above interval contained 2021 genes, 20 of which were involved in photosynthesis, but no SGR or genes with similar functions were identified. However, the published faba bean vfSGR was located within the vfGC candidate interval, confirming that our localization interval was reliable. The above findings provided further clues for the fine localization of genes regulating green cotyledons and the development of molecular linked markers in faba bean.

Candidate genes related to first pod height (FPH) traits in faba bean plants are crucial for mechanised breeding. However, reports on quantitative trait locus (QTL) mapping related to the FPH of faba bean are few, thus limiting the high-quality development of the faba bean industry to a certain extent. The identification and screening of candidate genes related to FPH is extremely urgent for the advancement of mechanised breeding for faba bean. In this study, a high-density genetic linkage map was constructed using genotyping-by-sequencing (GBS) of an F₃ population and QTLs (genes) related to FPH were identified. The genetic linkage map contained seven linkage groups with 3012 SNP markers with an overall length of 4089.13 centimorgan (cM) and an average marker density of 1.36 cM. Thirty-eight QTLs for the first pod node (FPN) and FPH were identified (19 each for FPN and FPH). The 19 QTLs associated with FPN were located on chromosomes 1L, 1S, 2, 3, 4, 5, and 6; the 19 QTLs associated with FPH were located on chromosomes 1L, 1S, 2, 3, 5, and 6. There was a co-localisation interval of qFPN6-1 and qFPH6-1 on chromosome 6. By annotating the QTL qFPH6-1 interval, 36 genes that may be related to FPH were identified, these genes are related to plant growth and development. The results provide a basis for the precise location of QTLs related to FPH and could accelerate the breeding of faba bean varieties adapted to mechanised harvesting.

Novel germplasm resources are the key to crop breeding, with their genetic diversity and population structure analysis being highly significant for future faba bean breeding. We genotyped 410 global faba bean accessions using the 130K targeted next-generation sequencing (TNGS) genotyping platform, resulting in a total of 38,111 high-quality SNP loci by high-standard filtering. We found the polymorphism information content (PIC) and Nei’s gene diversity were 0.0905–0.3750 and 0.0950–0.5000, with averages of 0.2471 and 0.3035, respectively. After evaluating the genetic diversity of 410 accessions using Nei’s gene diversity and PIC, on the basis of their geographical origin (continent) and structure-analysis-inferred subpopulations, we found that the faba bean accessions from Asia (except China) and Europe had rich genetic diversity, while those from the winter sowing area of China were low. The 410 faba bean accessions were divided into four subpopulations according to population structure analysis and clustering analysis based on Nei’s (1972) genetic distance using the neighbor-joining (NJ) method. However, the same subpopulation contained materials from different geographical origins, thereby indicating that the gene flow or introgression occurred among the accessions. Results from NJ clustering based on shared allele genetic distance indicated that the 410 accessions were divided into three groups according to their dissemination routes. The genetic diversity analysis results demonstrated that the genetic relationships among the faba bean groups with similar ecological environments and geographic origins in neighboring regions or countries were closer and frequently found within the same group, while genetic variation among individuals was the main source of their total genetic variation.