Genomic Prediction of Biomass Yield in Two Selection Cycles of a Tetraploid Alfalfa Breeding Population

Li, Xuehui; Wei, Yanling; Acharya, Ananta; Hansen, Julie L.; Crawford, Jamie; Viands, D. R.; Michaud, R.; Claessens, Annie; Brummer, E. Charles

doi:10.3835/plantgenome2014.12.0090

Cited by 82 publications

(71 citation statements)

References 60 publications

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“…GBS and other genomic investigations allowed the identification of QTL influencing various agronomic traits in alfalfa, such as biomass yield [20–22], aluminium tolerance [23], drought tolerance [24], salt tolerance [25], freezing tolerance [26] and biomass yield under drought stress [27]. However, there is a paucity of studies regarding alfalfa forage quality traits.…”

Section: Introductionmentioning

confidence: 99%

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

Biazzi¹,

N.²,

Pecetti³

et al. 2017

PLoS ONE

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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.

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Section: Introductionmentioning

confidence: 99%

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

Biazzi¹,

N.²,

Pecetti³

et al. 2017

PLoS ONE

Self Cite

123

114

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“…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).…”

Section: Discussionmentioning

confidence: 99%

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

Casler

2018

Crop Science

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Increases in biomass yield of switchgrass (Panicum virgatum L.) have been achieved, but the rate of gain has been slow and would benefit from improved efficiency of selection methods. Dry matter (DM) determinations at the time of harvest are a traditional method to adjust fresh matter yield (FMY) to a DM basis. The purpose of this study was to determine if DM determinations in switchgrass yield evaluations are necessary or unnecessary. Data from 219 trial‐years of 11 published experiments were used to evaluate the value of DM adjustment. Heritability for FMY and dry biomass yield (DBY) were similar, and the genetic correlation between these two traits was >0.8 for 96.7% of the trial‐years. The direct effect of FMY on DBY was three to four times greater than the direct effect of DM concentration. Because DM determination requires a larger field crew at the time of harvest, the use of FMY as a selection criterion requires significantly less labor than DBY at harvest time. Tripling the number of families evaluated and eliminating the DM step would increase the expected genetic gain for DBY by 17%. However, decreasing the number of replicates per family while eliminating the DM step would undermine the gains in efficiency due to reduced heritability for FMY. Although the risk of using FMY is low, achieving this increase in efficiency requires a serious commitment to evaluating a very large number of replicated families in each generation, an effort that may be beyond the ability and scope of most breeding programs.

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“…Such germplasm has been generated to a limited extent using conventional breeding approaches (Melton et al, 1989;Ray et al, 2012). DNA marker-assisted breeding using conventional QTL introgression methods, or genomic selection strategies (Li and Brummer, 2012;Li et al, 2015), can subsequently be used to introgress desirable QTL and increase the frequency of targeted favorable alleles in elite populations. DNA marker-assisted breeding using conventional QTL introgression methods, or genomic selection strategies (Li and Brummer, 2012;Li et al, 2015), can subsequently be used to introgress desirable QTL and increase the frequency of targeted favorable alleles in elite populations.…”

Section: Researchmentioning

confidence: 99%

“…Opportunities to accelerate improvement of alfalfa drought resilience may also be realized through the identification of favorable DNA marker alleles located at, or near, quantitative trait loci (QTL) associated with drought resistance traits and forage productivity during drought stress (Ray et al, 2015;Zhang et al, 2015). DNA marker-assisted breeding using conventional QTL introgression methods, or genomic selection strategies (Li and Brummer, 2012;Li et al, 2015), can subsequently be used to introgress desirable QTL and increase the frequency of targeted favorable alleles in elite populations.…”

Section: Researchmentioning

confidence: 99%

Genetic Mapping of Water Use Efficiency and Carbon and Nitrogen Metabolism in Drought‐Stressed Alfalfa

et al. 2019

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Identifying quantitative trait loci (QTL) associated with alfalfa (Medicago sativa L.) shoot biomass (SB), water use efficiency, and C and N metabolism can resolve potential target sites for selection and provide new insight into genetic relationships that may exist between key traits in water‐limited environments. The goal of this study was to utilize a tetraploid (2n = 4x = 32) BC1 mapping population and a genetic map based on 334 molecular markers to detect QTL associated with SB, C isotope discrimination (CID), and C and N content during drought stress. Half‐sib families derived from 96 BC1 individuals were evaluated for the SB trait in seeded plots near Las Cruces, NM, during two water‐stressed forage regrowth cycles in each of 3 yr (2005–2007). High costs associated with CID phenotyping precluded evaluation of the entire population. Therefore, in 2006 and 2007, shoot tissue samples for CID, C content, and N content measurements were collected from a subset of 29 families that exhibited extreme SB phenotypes in 2005. Significant genotype effects were observed among these families for SB and CID in both years and C and N content in 2006. Interval mapping identified QTL for all traits. Phenotypic effects of QTL supported significant positive genetic correlations detected between SB and CID, and between C and N content. Estimated QTL positions within the M. truncatula Gaertn. genome sequence assembly encompassed multiple candidate genes affiliated with stomatal development, cuticular wax biosynthesis, C and N metabolism, and abiotic stress response.

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Genomic Prediction of Biomass Yield in Two Selection Cycles of a Tetraploid Alfalfa Breeding Population

Cited by 82 publications

References 60 publications

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

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

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

Genetic Mapping of Water Use Efficiency and Carbon and Nitrogen Metabolism in Drought‐Stressed Alfalfa

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