Abstract
Genetic progress for forage quality has been poor in alfalfa (Medicago sativa 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 M. truncatula-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.
Highlights
Alfalfa (Medicago sativa L. subsp. sativa) is the most-grown perennial forage legume globally [1], owing to its high yield, stress tolerance and forage quality and the positive effects on soil fertility of its cultivation [2]
The autumn growing condition (C3) exhibited definitely better forage quality than two conditions harvested in summer (C1 and C2), owing to markedly higher leaf-to-stem ratio and to more favourable stem characteristics such as higher protein and NDF digestibility after hours (NDFD) and lower neutral detergent fiber (NDF) and acid detergent lignin (ADL) concentration (Table 1)
Fully-irrigated (C1) and irrigationsuspended (C2) summer growing conditions showed no difference for forage quality traits except for leaf protein concentration and leaf NDFD, which were lower in C2 (Table 1)
Summary
Alfalfa (Medicago sativa L. subsp. sativa) is the most-grown perennial forage legume globally [1], owing to its high yield, stress tolerance and forage quality and the positive effects on soil fertility of its cultivation [2]. Sativa) is the most-grown perennial forage legume globally [1], owing to its high yield, stress tolerance and forage quality and the positive effects on soil fertility of its cultivation [2]. It is widely adopted in feeding of dairy cows, where, poor genetic progress for forage digestibility and forage intake traits limits its full potential of utilization [1]. Various studies have revealed the presence of variation for forage quality traits, within cultivars [12, 13] Exploiting this variation requires the evaluation of large numbers of genotypes for forage quality parameters across various growing conditions [14], which is both costly and time intensive. The development of selection procedures based on molecular marker information could radically streamline and accelerate forage quality improvement
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