Accelerating biomass improvement is a major goal of
- NSF-PAR ID:
- 10469562
- Author(s) / Creator(s):
- ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- GCB Bioenergy
- Volume:
- 15
- Issue:
- 11
- ISSN:
- 1757-1693
- Format(s):
- Medium: X Size: p. 1355-1372
- Size(s):
- ["p. 1355-1372"]
- Sponsoring Org:
- National Science Foundation
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Abstract Miscanthus is a high‐yielding bioenergy crop that is broadly adapted to temperate and tropical environments. Commercial cultivation ofMiscanthus is predominantly limited to a single sterile triploid clone ofMiscanthus ×giganteus , a hybrid betweenMiscanthus sacchariflorus andM. sinensis. To expand the genetic base ofM. ×giganteus , the substantial diversity within its progenitor species should be used for cultivar improvement and diversification. Here, we phenotyped a diversity panel of 605M. sacchariflorus from six previously described genetic groups and 27M. ×giganteus genotypes for dry biomass yield and 16 yield‐component traits, in field trials grown over 3 years at one subtropical location (Zhuji, China) and four temperate locations (Foulum, Denmark; Sapporo, Japan; Urbana, Illinois; and Chuncheon, South Korea). There was considerable diversity in yield and yield‐component traits among and within genetic groups ofM. sacchariflorus , and across the five locations. Biomass yield ofM. sacchariflorus ranged from 0.003 to 34.0 Mg ha−1in year 3. Variation among the genetic groups was typically greater than within, so selection of genetic group should be an important first step for breeding withM. sacchariflorus . The Yangtze 2x genetic group (=ssp.lutarioriparius ) ofM. sacchariflorus had the tallest and thickest culms at all locations tested. Notably, the Yangtze 2x genetic group's exceptional culm length and yield potential were driven primarily by a large number of nodes (>29 nodes culm−1average over all locations), which was consistent with the especially late flowering of this group. The S Japan 4x, the N China/Korea/Russia 4x, and the N China 2x genetic groups were also promising genetic resources for biomass yield, culm length, and culm thickness, especially for temperate environments. Culm length was the best indicator of yield potential inM. sacchariflorus . These results will inform breeders' selection ofM. sacchariflorus genotypes for population improvement and adaptation to target production environments. -
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Abstract Background Genome wide association (GWA) studies demonstrate linkages between genetic variants and traits of interest. Here, we tested associations between single nucleotide polymorphisms (SNPs) in rice (
Oryza sativa ) and two root hair traits, root hair length (RHL) and root hair density (RHD). Root hairs are outgrowths of single cells on the root epidermis that aid in nutrient and water acquisition and have also served as a model system to study cell differentiation and tip growth. Using lines from the Rice Diversity Panel-1, we explored the diversity of root hair length and density across four subpopulations of rice (aus ,indica ,temperate japonica , andtropical japonica ). GWA analysis was completed using the high-density rice array (HDRA) and the rice reference panel (RICE-RP) SNP sets.Results We identified 18 genomic regions related to root hair traits, 14 of which related to RHD and four to RHL. No genomic regions were significantly associated with both traits. Two regions overlapped with previously identified quantitative trait loci (QTL) associated with root hair density in rice. We identified candidate genes in these regions and present those with previously published expression data relevant to root hair development. We re-phenotyped a subset of lines with extreme RHD phenotypes and found that the variation in RHD was due to differences in cell differentiation, not cell size, indicating genes in an associated genomic region may influence root hair cell fate. The candidate genes that we identified showed little overlap with previously characterized genes in rice and
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Abstract Missing heritability in genome-wide association studies defines a major problem in genetic analyses of complex biological traits 1,2 . The solution to this problem is to identify all causal genetic variants and to measure their individual contributions 3,4 . Here we report a graph pangenome of tomato constructed by precisely cataloguing more than 19 million variants from 838 genomes, including 32 new reference-level genome assemblies. This graph pangenome was used for genome-wide association study analyses and heritability estimation of 20,323 gene-expression and metabolite traits. The average estimated trait heritability is 0.41 compared with 0.33 when using the single linear reference genome. This 24% increase in estimated heritability is largely due to resolving incomplete linkage disequilibrium through the inclusion of additional causal structural variants identified using the graph pangenome. Moreover, by resolving allelic and locus heterogeneity, structural variants improve the power to identify genetic factors underlying agronomically important traits leading to, for example, the identification of two new genes potentially contributing to soluble solid content. The newly identified structural variants will facilitate genetic improvement of tomato through both marker-assisted selection and genomic selection. Our study advances the understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding.more » « less
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