Abstract
Soil salinity is a growing problem in world production agriculture. Continued improvement in crop salt tolerance will require the implementation of innovative breeding strategies such as marker-assisted selection (MAS) and genomic selection (GS). Genetic analyses for yield and vigor traits under salt stress in alfalfa breeding populations with three different phenotypic datasets was assessed. Genotype-by-sequencing (GBS) developed markers with allele dosage and phenotypic data were analyzed by genome-wide association studies (GWAS) and GS using different models. GWAS identified 27 single nucleotide polymorphism (SNP) markers associated with salt tolerance. Mapping SNPs markers against the Medicago truncatula reference genome revealed several putative candidate genes based on their roles in response to salt stress. Additionally, eight GS models were used to estimate breeding values of the training population under salt stress. Highest prediction accuracies and root mean square errors were used to determine the best prediction model. The machine learning methods (support vector machine and random forest) performance best with the prediction accuracy of 0.793 for yield. The marker loci and candidate genes identified, along with optimized GS prediction models, were shown to be useful in improvement of alfalfa with enhanced salt tolerance. DNA markers and the outcome of the GS will be made available to the alfalfa breeding community in efforts to accelerate genetic gains, in the development of biotic stress tolerant and more productive modern-day alfalfa cultivars.
Highlights
The impacts of soil salinization on world agriculture will become more pervasive and severe in the future
Biallelic single nucleotide variants (SNVs) were transformed into GWASpoly format with Next Generation Sequencing Experience Platform (NGSEP) software v 3.3.3 and were subjected to genome-wide association studies (GWAS) and genomic selection (GS) analysis
Compared with previous studies in alfalfa, our work provided a methodology that notably increases the accuracy of GS prediction and helps in making breeding decisions based on genotypic data
Summary
The impacts of soil salinization on world agriculture will become more pervasive and severe in the future. In areas where the water table is near the surface, a continuous column of water can form between the surface and the (saline) water table. When this occurs, evapotranspiration at the surface creates a “wicking”. Irrigated agriculture can cause salt levels to increase over time, mainly from use of high-salt irrigation water. This problem is exacerbated in areas with poor drainage. Increasing a crops’ salt tolerance can potentially reduce water usage, irrigation costs, and environmental impacts
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