Accuracy of genome-enabled predictions for alfalfa forage quality traits based on five regression models.

<p>Pearson’s correlation between actual and predicted phenotypes (average of 500 repetitions of 10-fold cross validation). L/S ratio, leaf-to-stem ratio; L-NDF, leaf neutral detergent fiber; L-ADL, leaf acid detergent lignin; L-CP, leaf crude protein; L-NDFD, leaf <i>in vitro</i> NDF digestibility at 24 hours; S-NDF, stem neutral detergent fiber; S-ADL, stem acid detergent lignin; S-CP, stem crude protein; S-NDFD, stem <i>in vitro</i> NDF digestibility at 24 hours.</p

Genome-Wide Association Mapping and Genomic Selection for Alfalfa (<i>Medicago sativa</i>) Forage Quality Traits

<div><p>Genetic progress for forage quality has been poor in alfalfa (<i>Medicago sativa</i> L.), the most-grown forage legume worldwide. This study aimed at exploring opportunities for marker-assisted selection (MAS) and genomic selection of forage quality traits based on breeding values of parent plants. Some 154 genotypes from a broadly-based reference population were genotyped by genotyping-by-sequencing (GBS), and phenotyped for leaf-to-stem ratio, leaf and stem contents of protein, neutral detergent fiber (NDF) and acid detergent lignin (ADL), and leaf and stem NDF digestibility after 24 hours (NDFD), of their dense-planted half-sib progenies in three growing conditions (summer harvest, full irrigation; summer harvest, suspended irrigation; autumn harvest). Trait-marker analyses were performed on progeny values averaged over conditions, owing to modest germplasm × condition interaction. Genomic selection exploited 11,450 polymorphic SNP markers, whereas a subset of 8,494 <i>M</i>. <i>truncatula</i>-aligned markers were used for a genome-wide association study (GWAS). GWAS confirmed the polygenic control of quality traits and, in agreement with phenotypic correlations, indicated substantially different genetic control of a given trait in stems and leaves. It detected several SNPs in different annotated genes that were highly linked to stem protein content. Also, it identified a small genomic region on chromosome 8 with high concentration of annotated genes associated with leaf ADL, including one gene probably involved in the lignin pathway. Three genomic selection models, i.e., Ridge-regression BLUP, Bayes B and Bayesian Lasso, displayed similar prediction accuracy, whereas SVR-lin was less accurate. Accuracy values were moderate (0.3–0.4) for stem NDFD and leaf protein content, modest for leaf ADL and NDFD, and low to very low for the other traits. Along with previous results for the same germplasm set, this study indicates that GBS data can be exploited to improve both quality traits (by genomic selection or MAS) and forage yield.</p></div

Mean values of forage quality traits recorded on dry leaves and stems of 154 alfalfa half-sib progenies in three growing conditions (C1, C2, C3).

<p>Mean values of forage quality traits recorded on dry leaves and stems of 154 alfalfa half-sib progenies in three growing conditions (C1, C2, C3).</p

Physical map of annotated genes and markers associated with alfalfa leaf (L) and stem (S) quality traits.

<p>Blue, neutral detergent fiber; red, acid detergent lignin; black, crude protein; green, <i>in vitro</i> NDF digestibility at 24 hours. Major associations (whose definition is given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0169234#pone.0169234.t003" target="_blank">Table 3</a>) are bold underlined. The blue box highlights a portion of chromosome 8 with high concentration of significant associations. Marker positions were based on the reference genome of <i>M</i>. <i>truncatula Mt4</i>.<i>0v1</i>.</p

Annotated genes or SNP markers associated with alfalfa forage quality traits with highest association score (-Log₁₀(<i>P</i>-value) > 4.0) and coefficient of determination (<i>R</i>² ≥ 0.10).

<p>Annotated genes or SNP markers associated with alfalfa forage quality traits with highest association score (-Log₁₀(<i>P</i>-value) > 4.0) and coefficient of determination (<i>R</i>² ≥ 0.10).</p

Range of progeny mean values, genetic coefficient of variation (<i>CV</i>_<i>g</i>) in three growing conditions (C1, C2, C3), <i>F</i> test results for overall progeny × condition (P×C) interaction, genetic correlation for progeny responses across pairs of conditions, and broad-sense heritability on a mean progeny basis over conditions (<i>h²_B</i>), for forage quality traits recorded on dry leaves and stems of 154 alfalfa half-sib progenies.

<p>Range of progeny mean values, genetic coefficient of variation (<i>CV</i>_<i>g</i>) in three growing conditions (C1, C2, C3), <i>F</i> test results for overall progeny × condition (P×C) interaction, genetic correlation for progeny responses across pairs of conditions, and broad-sense heritability on a mean progeny basis over conditions (<i>h²_B</i>), for forage quality traits recorded on dry leaves and stems of 154 alfalfa half-sib progenies.</p