Winter hardiness of <i>Miscanthus</i> (III): Genome‐wide association and genomic prediction for overwintering ability in <i>Miscanthus sinensis</i>

Dong, Hongxu; Clark, Lindsay V.; Lipka, Alexander E.; Brummer, Joe E.; Głowacka, Katarzyna; Hall, Mark E.; Heo, Kweon; Jin, Xiaoli; Peng, Junhua; Yamada, Toshihiko; Ghimire, Bimal Kumar; Yoo, Ji Hye; Yu, Chang Yeon; Zhao, Hua; Long, Stephen P.; Sacks, Erik J.

doi:10.1111/gcbb.12615

Cited by 7 publications

(9 citation statements)

References 87 publications

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“…For example, in Miscanthus, another well-known bioenergy biomass crop, substantial phenotypic variations of overwintering ability (i.e. transition from winter dormancy to spring regrowth, a trait analogous to spring green-up in this study) have been reported in a large M. sinensis germplasm panel (Dong et al 2019a), and QTL mapping across multiple populations revealed numerous QTLs that are unique to speci c populations (Dong et al 2018;Dong et al 2019b). Therefore, more genetic mapping studies are needed to understand the rich genetic diversity underlying agronomic traits in switchgrass, particularly the underexplored yet important traits such as spring green-up and plant vigor.…”

Section: Introductionmentioning

confidence: 63%

Mapping QTLs for spring green-up, plant vigor, and plant biomass in two lowland switchgrass populations

Chang

Dong

Bai³

et al. 2022

Mol Breeding

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Switchgrass ( Panicum virgatum L.) is an important perennial cellulosic bioenergy species. Identi cation of quantitative trait loci (QTL) controlling important developmental traits is valuable to understanding the genetic basis and breeding high-yielding cultivars. One F 1 hybrid population consisting of 176 individuals derived from NL94 ( ) × SL93 ( ), and one S 1 ( rst-generation selfed) population of 265 individuals from NL94, were used to study spring greenup, plant vigor and plant biomass in switchgrass. Both populations showed signi cant variations for genotype, and genotype by environment interactions for the three traits. Plant vigor had strong and positive correlations with plant biomass in both populations. Broad sense heritability estimates of plant vigor ranged from 0.46 to 0.74 and 0.45 to 0.74 in the hybrid and selfed population, respectively. Spring green-up had similar heritability estimates in these two populations (0.42-0.78 in hybrid population, 0.47-0.82 in selfed population). The heritability of plant biomass was above 0.5 (0.54-0.64 in hybrid population, 0.64-0.74 in selfed population). Fifteen and four QTLs were detected for spring green-up in the hybrid and selfed population, respectively. Six and four QTLs were detected for plant vigor in the hybrid and selfed population, respectively. Three QTLs in the hybrid population and one QTL in the selfed population were identi ed for plant biomass. This study provided new information in understanding the genetic control of biomass components and demonstrated substantial heterotic vigor that could be explored for breeding hybrid cultivars in switchgrass.

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Section: Introductionmentioning

confidence: 63%

Mapping QTLs for spring green-up, plant vigor, and plant biomass in two lowland switchgrass populations

Chang

Dong

Bai³

et al. 2022

Mol Breeding

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“…Given that population structure can inflate genomic prediction accuracies (Guo et al, 2014; Riedelsheimer et al, 2012), we accounted for sub‐structure in the M. sacchariflorus germplasm panel by fitting a linear model where the trait LS means were the response variable, and the genetic groups were the explanatory variable using Equation (4):

y goodbreak= μ goodbreak+ D goodbreak+ e,

where

y

is the LS means calculated from Equations (1) or (2),

μ

is the grand mean, D is the genetic group of M. sacchariflorus previously identified by Clark et al (2018) for this diversity panel, and

e

is the residual effect. The residuals from the model were used as phenotypic values in genomic prediction as previously done in Clark, Dwiyanti, et al (2019), Dong et al (2019) and Lipka et al (2014). We performed genomic prediction for each trait, and all 590 accessions, with LS means estimated for ZJU, northern locations (HU + UI + KNU), and all locations (HU + UI + KNU + ZJU).…”

Section: Methodsmentioning

confidence: 99%

“…Previous GWAS and genomic prediction efforts in Miscanthus have focused on M. sinensis (Clark, Dwiyanti, et al, 2019; Davey et al, 2017; Dong et al, 2019; Nie et al, 2016; Slavov et al, 2014; Teng et al, 2017; Zhao, Wang, et al, 2013). However, GWAS and genomic prediction have been largely unexplored in M. sacchariflorus , with only two prior studies in the literature (Clark et al, 2016; Olatoye et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide association and genomic prediction for yield and component traits of Miscanthus sacchariflorus

Njuguna,

Clark,

Lipka

et al. 2023

GCB Bioenergy

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Accelerating biomass improvement is a major goal of Miscanthus breeding. The development and implementation of genomic‐enabled breeding tools, like marker‐assisted selection (MAS) and genomic selection, has the potential to improve the efficiency of Miscanthus breeding. The present study conducted genome‐wide association (GWA) and genomic prediction of biomass yield and 14 yield‐components traits in Miscanthus sacchariflorus. We evaluated a diversity panel with 590 accessions of M. sacchariflorus grown across 4 years in one subtropical and three temperate locations and genotyped with 268,109 single‐nucleotide polymorphisms (SNPs). The GWA study identified a total of 835 significant SNPs and 674 candidate genes across all traits and locations. Of the significant SNPs identified, 280 were localized in mapped quantitative trait loci intervals and proximal to SNPs identified for similar traits in previously reported Miscanthus studies, providing additional support for the importance of these genomic regions for biomass yield. Our study gave insights into the genetic basis for yield‐component traits in M. sacchariflorus that may facilitate marker‐assisted breeding for biomass yield. Genomic prediction accuracy for the yield‐related traits ranged from 0.15 to 0.52 across all locations and genetic groups. Prediction accuracies within the six genetic groupings of M. sacchariflorus were limited due to low sample sizes. Nevertheless, the Korea/NE China/Russia (N = 237) genetic group had the highest prediction accuracy of all genetic groups (ranging 0.26–0.71), suggesting that with adequate sample sizes, there is strong potential for genomic selection within the genetic groupings of M. sacchariflorus. This study indicated that MAS and genomic prediction will likely be beneficial for conducting population‐improvement of M. sacchariflorus.

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“…Miscanthus has been considered to be a promising second-generation bioenergy crop [ 15 ]. The genus is naturally distributed in a wide climatic range from tropical areas of east Asia to ~50 °N in eastern Russia [ 16 , 17 ]. Therefore, Miscanthus species have extensive genetic diversity for energy crop development.…”

Section: Introductionmentioning

confidence: 99%

Water Use Efficiency and Stress Tolerance of the Potential Energy Crop Miscanthus lutarioriparius Grown on the Loess Plateau of China

Zhao

Kang

Wang

et al. 2021

Plants

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As a potential energy crop with high biomass yield, Miscanthus lutarioriparius (M. lutarioriparius), endemic to the Long River Range in central China, needs to be investigated for its acclimation to stressful climatic and soil conditions often found on the marginal land. In this study, traits related to acclimation and yield, including survival rates, plant height (PH), stem diameter (SD), tiller number (TN), water use efficiency (WUE), and photosynthetic rates (A), were examined for 41 M. lutarioriparius populations that transplanted to the arid and cold Loess Plateau of China. The results showed that the average survival rate of M. lutarioriparius populations was only 4.16% over the first winter but the overwinter rate increased to 35.03% after the second winter, suggesting that plants having survived the first winter could have acclaimed to the low temperature. The strikingly high survival rates over the second winter were found to be 95.83% and 80.85%, respectively, for HG18 and HG39 populations. These populations might be especially valuable for the selection of energy crops for such an area. Those individuals surviving for the two consecutive winters showed significantly higher WUE than those measured after the first winter. The high WUE and low stomatal conductance (gs) observed in survived individuals could have been responsible for their acclimation to this new and harsh environment. A total of 61 individuals with productive growth traits and strong resistance to cold and drought were identified for further energy crop development. This study showed that the variation of M. lutarioriparius held great potential for developing energy crops following continuous field selection.

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Winter hardiness of Miscanthus (III): Genome‐wide association and genomic prediction for overwintering ability in Miscanthus sinensis

Cited by 7 publications

References 87 publications

Mapping QTLs for spring green-up, plant vigor, and plant biomass in two lowland switchgrass populations

Mapping QTLs for spring green-up, plant vigor, and plant biomass in two lowland switchgrass populations

Genome‐wide association and genomic prediction for yield and component traits of Miscanthus sacchariflorus

Water Use Efficiency and Stress Tolerance of the Potential Energy Crop Miscanthus lutarioriparius Grown on the Loess Plateau of China

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