Identification of Single-Nucleotide Polymorphic Loci Associated with Biomass Yield under Water Deficit in Alfalfa (Medicago sativa L.) Using Genome-Wide Sequencing and Association Mapping

Abstract

Alfalfa is a worldwide grown forage crop and is important due to its high biomass production and nutritional value. However, the production of alfalfa is challenged by adverse environmental factors such as drought and other stresses. Developing drought resistance alfalfa is an important breeding target for enhancing alfalfa productivity in arid and semi-arid regions. In the present study, we used genotyping-by-sequencing and genome-wide association to identify marker loci associated with biomass yield under drought in the field in a panel of diverse germplasm of alfalfa. A total of 28 markers at 22 genetic loci were associated with yield under water deficit, whereas only four markers associated with the same trait under well-watered condition. Comparisons of marker-trait associations between water deficit and well-watered conditions showed non-similarity except one. Most of the markers were identical across harvest periods within the treatment, although different levels of significance were found among the three harvests. The loci associated with biomass yield under water deficit located throughout all chromosomes in the alfalfa genome agreed with previous reports. Our results suggest that biomass yield under drought is a complex quantitative trait with polygenic inheritance and may involve a different mechanism compared to that of non-stress. BLAST searches of the flanking sequences of the associated loci against DNA databases revealed several stress-responsive genes linked to the drought resistance loci, including leucine-rich repeat receptor-like kinase, B3 DNA-binding domain protein, translation initiation factor IF2, and phospholipase-like protein. With further investigation, those markers closely linked to drought resistance can be used for MAS to accelerate the development of new alfalfa cultivars with improved resistance to drought and other abiotic stresses.

Identification of genetic loci associated with forage quality in response to water deficit in autotetraploid alfalfa (Medicago sativa L.)

“…Cutting frequently for high-quality forage always induce [19]. In previous study, we identified 22 markers associated with alfalfa yield under different water deficit conditions [20]. Of those, 15 markers were identical with the quality-related markers identified in this study, indicating that these loci might participate in controlling both the yield and quality traits in alfalfa.…”

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.…”

“…Several QTLs for important traits such as winter hardiness, fall growth and freezing injury ( Brouwer et al, 2000 ), biomass production ( Robins et al, 2007a ), forage yield ( Robins et al, 2007b ; McCord et al, 2014 ), plant height and regrowth ( Robins et al, 2007b ), persistence tolerance ( Robins et al, 2008 ) and, lodging resistance and spring vigor traits ( McCord et al, 2014 ) have been identified in tetraploid alfalfa ( Table 2 ). In addition, Ray et al (2015) identified small-effect QTLs controlling biomass yield under drought in tetraploid alfalfa ( Table 2 ).…”

Adjustment of Biomass Yield to a Dry Matter Basis in Switchgrass Breeding: A Necessity or a Nuisance?

“…5. There are precedents for using FMY as a selection criterion in alfalfa ( Medicago sativa L.) breeding programs, either with an average DM adjustment from a small random sample of plots (Li et al, 2015) or without any DM adjustment (Yu, 2017). In perennial ryegrass ( Lolium perenne L.), FMY is routinely used as the principal selection criterion for forage yield plots under both conservation and frequent‐harvest managements, owing to relationships between FMY and DMY that are similar to those observed in the current study (Conaghan et al, 2008).…”