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Identification of loci controlling forage yield and nutritive value in diploid alfalfa using GBS-GWAS

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We attempted to identify genomic regions controlling forage yield and nutritive value in alfalfa. Several candidate genes and associated genetic markers were identified that could potentially be useful for alfalfa breeding to more efficiently develop improved cultivars.

Abstract

Alfalfa is one of the most widely cultivated forage legumes worldwide and improving alfalfa forage yield and nutritive value is a major global breeding goal. Genotyping-by-sequencing (GBS) provides cost-effective molecular marker genotyping for genome-wide association studies (GWAS). Using more than 15,000 genome-wide single nucleotide polymorphisms (SNP) identified from GBS, we conducted a GWAS to investigate forage yield and nutritive value-related traits. We have detected a number of associations for all the traits evaluated and a number of associations detected were located on the Medicago truncatula genome. The SNP in a coding region of a cell wall biosynthesis gene was associated with several cell wall-related traits, and we suggest that it may be the causative polymorphism. Two other SNPs residing in meristematic development and early growth genes were found to associate with the total biomass yield. None of the SNPs associated with regrowth after harvest or with spring regrowth were mapped to the M. truncatula genome, possibly reflecting the fact that M. truncatula is an annual species related to alfalfa that typically has limited ability to regrow. The alleles we identify with the major impact on forage yield and nutritive value can be rapidly incorporated into our breeding program.

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Acknowledgments

We would like to thank to The Scientific and Technological Research Council of Turkey (TUBITAK) for supporting MŞ. This research was partially supported USDA-DOE Plant Feedstock Genomics for Bioenergy program awards #2006-35300-17224 and #2009-65504-05809 to E.C.B.

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Authors and Affiliations

  1. Bioengineering Department, Kafkas University, 36100, Kars, Turkey

    Muhammet Sakiroglu

  2. Department of Plant Sciences, Plant Breeding Center, The University of California, Davis, CA, 95616, USA

    E. Charles Brummer

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  1. Muhammet Sakiroglu
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  2. E. Charles Brummer
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Correspondence to Muhammet Sakiroglu.

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Additional information

Communicated by M. N. Nelson.

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122_2016_2782_MOESM1_ESM.png

Supplemental Fig. 1 Scree plot of the Principal Component Analyses of genotypic data from 362 individual genotypes. The X-axis indicates the principal component number and the Y axis indicates the proportion of the variance explained by each PC and the cumulative variance explained across PCs. (PNG 74 kb)

122_2016_2782_MOESM2_ESM.png

Supplemental Fig. 2 Quantile–quantile (Q–Q) plots for rest of the traits obtained by standard mixed linear model with both Q matrix and PCA correction. (a) arabinose (fall harvest), (b) arabinose (summer harvest), (c) glucose (fall harvest), (d) glucose (summer harvest), (e) NDF (fall harvest), (f) NDF (summer harvest), (g) regrowth (fall harvest), (h) regrowth (summer harvest), (i)stem thickness (summer harvest), (j) stem total mass ratio (fall harvest), (k) stem weight (fall harvest), (l) TNC (fall harvest), (m) TNC (summer harvest), (n) xylose (fall harvest), and (o) xylose (summer harvest) (PNG 353 kb)

122_2016_2782_MOESM3_ESM.jpg

Supplemental Fig. 3 Manhattan plots (mixed linear model) of mapped SNP markers associating with all the traits evaluated. (a) ADF (summer harvest), (b) ADL (fall harvest), (c) ADL (summer harvest), (d) arabinose (fall harvest), (e) arabinose (summer harvest), (f) glucose (fall harvest), (g) glucose (summer harvest), (h) NDF (summer harvest), (i) plant height (summer harvest), (j) regrowth (fall harvest), (k) regrowth (summer harvest), (l) spring regrowth (summer harvest), (m) stem thickness (summer harvest), (n) stem total mass ratio (fall harvest), (o) stem weight (fall harvest), (p) TNC (fall harvest), (q) TNC (summer harvest), (r) xylose (fall harvest), and (s) xylose (summer harvest) (JPEG 162 kb)

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Sakiroglu, M., Brummer, E.C. Identification of loci controlling forage yield and nutritive value in diploid alfalfa using GBS-GWAS. Theor Appl Genet 130, 261–268 (2017). https://doi.org/10.1007/s00122-016-2782-3

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