Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility
Common buckwheat ( Fagopyrum esculentum ) is an ancient crop with a world-wide distribution. Due to its excellent nutritional quality and high economic and ecological value, common buckwheat is becoming increasingly important throughout the world. The availability of a high-quality reference genome...
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Veröffentlicht in: | Molecular plant 2023-09, Vol.16 (9), p.1427-1444 |
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Sprache: | eng |
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Zusammenfassung: | Common buckwheat (
Fagopyrum esculentum
) is an ancient crop with a world-wide distribution. Due to its excellent nutritional quality and high economic and ecological value, common buckwheat is becoming increasingly important throughout the world. The availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat, but the high heterozygosity due to the outcrossing nature has greatly hindered the genome assembly. Here we report the assembly of a chromosome-scale high-quality reference genome of
F
.
esculentum
var.
homotropicum
, a homozygous self-pollinating variant of common buckwheat. Comparative genomics revealed that two cultivated buckwheat species, common buckwheat (
F
.
esculentum
) and Tartary buckwheat (
F
.
tataricum
), underwent metabolomic divergence and ecotype differentiation. The expansion of several gene families in common buckwheat, including
FhFAR
genes, is associated with its wider distribution than Tartary buckwheat. Copy number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary buckwheat. Furthermore, we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common buckwheat. Population and evolutionary genomics reveal genetic variation associated with environmental adaptability and floral development between Chinese and non-Chinese cultivated groups. Genome-wide association analyses of multi-year agronomic traits with the content of flavonoids revealed that
Fh05G014970
is a potential major regulator of flowering period, a key agronomic trait controlling the yield of outcrossing crops, and that
Fh06G015130
is a crucial gene underlying flavor-associated flavonoids. Intriguingly, we found that the gene translocation and sequence variation of
FhS-ELF3
contribute to the homomorphic self-compatibility of common buckwheat. Collectively, our results elucidate the genetic basis of speciation, ecological adaptation, fertility, and unique flavor of common buckwheat, and provide new resources for future genomics-assisted breeding of this economically important crop.
Despite the high ecological and economic value of common buckwheat, the availability of high-quality genomic resources is limited for this important crop. In this study, whole-genome sequencing and population genomics approaches were used to unravel the genetic basis of varied fl |
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ISSN: | 1674-2052 1752-9867 |
DOI: | 10.1016/j.molp.2023.08.013 |