Genome-Wide Association Mapping of Loci Associated with Plant Growth and Forage Production under Salt Stress in Alfalfa (Medicago sativa L.)

Abstract

Salinity tolerance is highly desirable to sustain alfalfa production in marginal lands that have been rendered saline. In this study, we used a diverse panel of 198 alfalfa accessions for mapping loci associated with plant growth and forage production under salt stress using genome-wide association studies (GWAS). The plants were genotyped using genotyping-by-sequencing (GBS). A greenhouse procedure was used for phenotyping four agronomic and physiological traits affected by salt stress, including dry weight (DW), plant height (PH), leaf chlorophyll content (LCC), and stomatal conductance (SC). For each trait, a stress susceptibility index (SSI) was used to evaluate plant performance under stressed and non-stressed conditions. Marker-trait association identified a total of 42 markers significantly associated with salt tolerance. They were located on all chromosomes except chromosome 2 based on the alignment of their flanking sequences to the reference genome (Medicago truncatula). Of those identified, 13 were associated with multiple traits. Several loci identified in the present study were also identified in previous reports. BLAST search revealed that 19 putative candidate genes linked to 24 significant markers. Among them, B3 DNA-binding protein, Thiaminepyrophosphokinase and IQ calmodulin-binding motif protein were identified among multiple traits in the present and previous studies. With further investigation, these markers and candidates would be useful for developing markers for marker-assisted selection in breeding programs to improve alfalfa cultivars with enhanced tolerance to salt stress.

Harnessing the Potential of Forage Legumes, Alfalfa, Soybean, and Cowpea for Sustainable Agriculture and Global Food Security

“…Many of these loci were found to overlap with the reported QTLs associated with biomass yield under drought. Similar marker-trait associations have been identified for forage yield and nutritive value ( Sakiroglu and Brummer, 2017 ), forage quality traits ( Biazzi et al, 2017 ), plant growth and forage production ( Liu and Yu, 2017 ), and biomass yield under water deficit conditions ( Yu, 2017 ; Table 2 ). Thus, genetic dissection of forage-related traits using advanced approaches could be useful in identifying loci that can be exploited through marker-assisted breeding to develop drought-resistant alfalfa cultivars with improved nutritive value.…”

Morphological, Physiological, and Genetic Responses to Salt Stress in Alfalfa: A Review

“…During alfalfa seed germination, a broad-sense heritability of the germination rate was observed at 0.60 at 0.5% (~8 dS m −1 NaCl) salt concentration, which decreased to 0.24 at 0.75% (~12 dS m −1 NaCl) and 0.27 at 1.0% (~17 dS m −1 NaCl) [104]. The broad-sense heritability of leaf chlorophyll content increased from 0.22 at 0 dS m −1 to 0.34 at 8 dS m −1 NaCl [105]. As salt-tolerant traits are genetically complex and multi-gene controlled, the development of genome-wide markers might be useful for conducting a genomic selection based on the predictive breeding values of genotypes.…”

“…Several studies have focused on the development of molecular markers associated with salt tolerance in alfalfa at different growth stages [93,94,[103][104][105]. The most significant salt tolerance markers during the germination stage were identified on chromosomes 1, 2, and 4, while the marker located on chromosome 6 overlapped with drought resistance [104,106].…”

GWAS Uncovers Differential Genetic Bases for Drought and Salt Tolerances in Sesame at the Germination Stage

“…It offers advantages over traditional linkage analyses, such as more accurate positioning and mapping, simultaneous assessments of multiple alleles at a locus and no requirement for linkage group construction [ 27 , 28 ]. It has been successfully applied in several crops such as alfalfa, Arabidopsis thaliana , soybean, maize, rice, asparagus bean, Brassica napus , etc., to dissect complex traits including salt and drought tolerance [ 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 ]. GWAS was also successfully applied in sesame to unravel the genetic basis of its high oil production and quality, and some other key agronomic traits by fully sequencing a population composed of 705 worldwide accessions [ 40 ].…”