Nested association mapping (NAM) populations are a powerful tool for investigating the genetic control of agronomically important traits and have been successfully used in self-pollinating crop species. Here, we present the first NAM population established in the outcrossing forage grass species Italian ryegrass (
Lolium multiflorum
Lam.), to dissect the genetic control of seed shattering. High and stable seed yields are essential for the commercial success of new cultivars. Seed shattering strongly reduces seed yield in Italian ryegrass, but has so far not been targeted in Italian ryegrass breeding programs.
The NAM population was based on one common and 23 diverse founder plants and consisted of 708 F
2
individuals. Reduced-representation sequencing (ddRAD) of the 708 F
2
individuals, combined with whole genome sequencing data of the 24 founder plants, yielded a total of 3,199,253 SNPs that were used for population structure analysis, parentship analysis and genome-wide association studies. Phenotypic data for seed shattering and seed yield-related traits, collected in three field trials, showed high phenotypic variance within the NAM population. A total of seven quantitative trait loci (QTL) were identified for seed shattering, seed yield, spike length, flag leaf length and flowering time. Within these QTL regions, one putative candidate gene for seed shattering and three putative candidate genes for flowering time were identified. For seed shattering, the significantly associated SNP within the gene
chr7.26897
, known to be involved in ripening-related pathways, explained 10.03% of the phenotypic variance.
The identified loci provide valuable resources for breeding. The QTL regions containing putative candidate genes identified within these loci offer promising targets for functional validation and demonstrate the effectiveness of NAM populations for elucidating the genetic architecture of complex traits in outcrossing forage grasses.
Jenny Kiesbauer, C. Grieder, Meril Sindelar et al.· BMC Plant Biology· 0 citations
Neglected and underutilized crops have great potential to diversify agroecosystems and human diets but require genetic improvement to make them economically viable alternatives to major crops. Common buckwheat (
Fagopyrum esculentum
Moench) is valued for its excellent nutritional quality, its ecological importance and its benefits on crop rotation and soil health. However, low and highly variable yields, along with uneven seed ripening, have limited the crop’s usage in farming systems, highlighting the need for improved varieties. The availability of genetic resources and detailed genetic characterization are prerequisites for efficient breeding strategies.
In this study, we elucidate the genetic diversity and phylogeography of a global germplasm collection comprising 170 common buckwheat accessions, including nine self-compatible accessions and eleven accessions with determinate growth habit. The collection was genetically characterized using double digest restriction-site associated DNA sequencing to generate accession-specific genome-wide allele frequency fingerprints (GWAFFs).
Using accurate and repeatable GWAFFs based on 52,182 genome sites, an analysis of genetic admixture revealed seven subclusters within the collection. Our results show that common buckwheat accessions collected in specific regions of the world usually trace back to a single subcluster. Western Europe is an exception, as accessions from several different subcluster have been integrated into local cropping and food systems.
These findings illustrate that most breeding programs for common buckwheat rely on only a fraction of the available genetic diversity. Therefore, the introduction of genetic material from different sources could increase the diversity of many local breeding programs. The precise genetic characterization of the collection with GWAFFs opens opportunities to apply modern breeding strategies such as genomics-assisted selection. True-to-type seed of 81 accessions of the collection were deposited in the Swiss National Gene Bank and are publicly available for cultivation and use in research and breeding.
Fabian Hess, Lukas Kronenberg, Steven Yates et al.· Frontiers in Plant Science· 0 citations
A sustainable approach to address climate change and increasing water demand in agriculture is breeding for plant functional traits that conserve water and enhance climate resilience. Stomata regulate plant-water relations and are promising targets for crop improvement. Here, we investigate the variation in stomatal density (SD) in a diverse apple population (Malus domestica Borkh.) consisting of 269 accessions. Genome-wide association studies identified robust associations with SD on chromosomes 2, 9, and 10 (classified as SNPs with p value higher than adjusted Bonferroni threshold of -log10(p) > 8.78 that were consistently identified across datasets). On chromosome 9, a candidate gene that negatively regulates stomatal development, EPIDERMAL PATTERNING FACTOR 1 (EPF1), was identified inside a genomic region of 241 kb determined by six robust associations. On chromosome 10, a positive regulator candidate gene, EPIDERMAL PATTERNING FACTOR LIKE 9 (STOMAGEN), was identified 1680 kb from the robust association. Identification of positive (STOMAGEN) and negative (EPF1) regulators of SD suggest potential antagonistic roles at the population scale in determining SD. On chromosome 2, a gene co-expression analysis identified a gene cluster containing both EPF1 and STOMAGEN together with a novel candidate gene, CYTOCHROME P450 (CYP77A4), that was located 544 kb from the robust association. The percentage of SD phenotypic variance explained by each robust association was between 7% and 10%. These findings provide a foundation for understanding SD variation at the population scale and opportunities to modulate SD by genomics-assisted breeding strategies.
Francesca Zuffa, M. Jung, Steven Yates et al.· Horticulture Research· 1 citation
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