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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 se...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512774/ https://www.ncbi.nlm.nih.gov/pubmed/37649255 http://dx.doi.org/10.1016/j.molp.2023.08.013 |
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author | Zhang, Kaixuan He, Yuqi Lu, Xiang Shi, Yaliang Zhao, Hui Li, Xiaobo Li, Jinlong Liu, Yang Ouyang, Yinan Tang, Yu Ren, Xue Zhang, Xuemei Yang, Weifei Sun, Zhaoxia Zhang, Chunhua Quinet, Muriel Luthar, Zlata Germ, Mateja Kreft, Ivan Janovská, Dagmar Meglič, Vladimir Pipan, Barbara Georgiev, Milen I. Studer, Bruno Chapman, Mark A. Zhou, Meiliang |
author_facet | Zhang, Kaixuan He, Yuqi Lu, Xiang Shi, Yaliang Zhao, Hui Li, Xiaobo Li, Jinlong Liu, Yang Ouyang, Yinan Tang, Yu Ren, Xue Zhang, Xuemei Yang, Weifei Sun, Zhaoxia Zhang, Chunhua Quinet, Muriel Luthar, Zlata Germ, Mateja Kreft, Ivan Janovská, Dagmar Meglič, Vladimir Pipan, Barbara Georgiev, Milen I. Studer, Bruno Chapman, Mark A. Zhou, Meiliang |
author_sort | Zhang, Kaixuan |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-10512774 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-105127742023-09-22 Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility Zhang, Kaixuan He, Yuqi Lu, Xiang Shi, Yaliang Zhao, Hui Li, Xiaobo Li, Jinlong Liu, Yang Ouyang, Yinan Tang, Yu Ren, Xue Zhang, Xuemei Yang, Weifei Sun, Zhaoxia Zhang, Chunhua Quinet, Muriel Luthar, Zlata Germ, Mateja Kreft, Ivan Janovská, Dagmar Meglič, Vladimir Pipan, Barbara Georgiev, Milen I. Studer, Bruno Chapman, Mark A. Zhou, Meiliang Mol Plant Research Article 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. Oxford University Press 2023-09-04 /pmc/articles/PMC10512774/ /pubmed/37649255 http://dx.doi.org/10.1016/j.molp.2023.08.013 Text en © 2023 The Author https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Research Article Zhang, Kaixuan He, Yuqi Lu, Xiang Shi, Yaliang Zhao, Hui Li, Xiaobo Li, Jinlong Liu, Yang Ouyang, Yinan Tang, Yu Ren, Xue Zhang, Xuemei Yang, Weifei Sun, Zhaoxia Zhang, Chunhua Quinet, Muriel Luthar, Zlata Germ, Mateja Kreft, Ivan Janovská, Dagmar Meglič, Vladimir Pipan, Barbara Georgiev, Milen I. Studer, Bruno Chapman, Mark A. Zhou, Meiliang Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility |
title | Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility |
title_full | Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility |
title_fullStr | Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility |
title_full_unstemmed | Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility |
title_short | Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility |
title_sort | comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512774/ https://www.ncbi.nlm.nih.gov/pubmed/37649255 http://dx.doi.org/10.1016/j.molp.2023.08.013 |
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