Nazzicari, N.; Franguelli, N.; Ferrari, B.; Pecetti, L.; Annicchiarico, P. The Effect of Genome Parametrization and SNP Marker Subsetting on Genomic Selection in Autotetraploid Alfalfa. Genes2024, 15, 449.
Nazzicari, N.; Franguelli, N.; Ferrari, B.; Pecetti, L.; Annicchiarico, P. The Effect of Genome Parametrization and SNP Marker Subsetting on Genomic Selection in Autotetraploid Alfalfa. Genes 2024, 15, 449.
Nazzicari, N.; Franguelli, N.; Ferrari, B.; Pecetti, L.; Annicchiarico, P. The Effect of Genome Parametrization and SNP Marker Subsetting on Genomic Selection in Autotetraploid Alfalfa. Genes2024, 15, 449.
Nazzicari, N.; Franguelli, N.; Ferrari, B.; Pecetti, L.; Annicchiarico, P. The Effect of Genome Parametrization and SNP Marker Subsetting on Genomic Selection in Autotetraploid Alfalfa. Genes 2024, 15, 449.
Abstract
Background: Alfalfa, the most economically important forage legume worldwide, features modest genetic progress due to long selection cycles and large extent of non-additive genetic variance associated with its autotetraploid genome.
Methods: To improve the efficiency of genomic selection in alfalfa, we explored the effects of genome parametrization (as autotetraploid and diploid dosage, plus allele ratios) and SNP marker subsetting (all available SNPs; only genic regions; only non-genic regions) on genomic regressions, together with various levels of filtering on reading depth and missing rates. We used Genotyping by Sequencing-generated data and focused on traits of different genetic complexity, i.e., dry biomass yield in moisture-favorable (FE) and drought stress (SE) environments, leaf size, and onset of flowering, assessed on 143 genotyped plants from a genetically-broad European reference population and their phenotyped half-sib progenies.
Results: On average, allele ratio improved the predictive ability compared with other genome parametrizations (+7.9% vs. tetraploid dosage, +12.6% vs. diploid dosage), SNP subsetting offered an advantage compared with any tested subsettings (+3.7% vs. genic regions, +7.6% vs. non-genic regions). However, when focusing on specific traits, different combinations of genome parametrization and subsetting reached better performances. We also released Legpipe2, a SNP calling pipeline tailored for reduced representation (GBS, RAD) medium-sized genotyping experiments.
Keywords
legumes; alfalfa; genomic selection; SNP calling pipeline; autotetraploidy; polyploidy; genome parametrization; SNP subsetting
Subject
Biology and Life Sciences, Agricultural Science and Agronomy
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
