The Distribution and Origins of Pyrus hopeiensis-“Wild Plant With Tiny Population” Using Whole Genome Resequencing

Pyrus hopeiensis is a valuable but endangered wild resource in the genus Pyrus. It has been listed as one of the 120 wild species with tiny population in China. The specie has been little studied. A preliminary study of propagation modes in P. hopeiensis was performed through seed propagation, hybri...

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Main Authors: Yongtan Li, Jun Zhang, Shijie Wang, Yiwen Zhang, Minsheng Yang
Format: Article
Language:English
Published: Frontiers Media S.A. 2021-06-01
Series:Frontiers in Plant Science
Subjects:
PCA
Online Access:https://www.frontiersin.org/articles/10.3389/fpls.2021.668796/full
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spelling doaj-898640485bb3475c859483c3fa220faa2021-06-17T10:59:03ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2021-06-011210.3389/fpls.2021.668796668796The Distribution and Origins of Pyrus hopeiensis-“Wild Plant With Tiny Population” Using Whole Genome ResequencingYongtan Li0Yongtan Li1Jun Zhang2Jun Zhang3Shijie Wang4Shijie Wang5Yiwen Zhang6Yiwen Zhang7Minsheng Yang8Minsheng Yang9Forest Department, Forestry College, Hebei Agricultural University, Baoding, ChinaHebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, ChinaForest Department, Forestry College, Hebei Agricultural University, Baoding, ChinaHebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, ChinaForest Department, Forestry College, Hebei Agricultural University, Baoding, ChinaHebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, ChinaForest Department, Forestry College, Hebei Agricultural University, Baoding, ChinaHebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, ChinaForest Department, Forestry College, Hebei Agricultural University, Baoding, ChinaHebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, ChinaPyrus hopeiensis is a valuable but endangered wild resource in the genus Pyrus. It has been listed as one of the 120 wild species with tiny population in China. The specie has been little studied. A preliminary study of propagation modes in P. hopeiensis was performed through seed propagation, hybridization, self-crossing trials, bud grafting, branch grafting, and investigations of natural growth. The results showed that the population size of P. hopeiensis was very small, the distribution range was limited, and the habitat was extremely degraded. In the wild population, natural hybridization and root tiller production were the major modes of propagation. Whole genome re-sequencing of the 23 wild and cultivated accessions from Pyrus species collected was performed using an Illumina HiSeq sequencing platform. The sequencing depth range was 26.56x−44.85x and the average sequencing depth was 32x. Phylogenetic tree and principal component analyses (PCA) based on SNPs showed that the wild Pyrus species, such as PWH06, PWH07, PWH09, PWH10, PWH13, and PWH17, were closely related to both P. hopeiensis HB-1 and P. hopeiensis HB-2. Using these results in combination with morphological characteristics, it speculated that P. hopeiensis populations may form a natural hybrid group with frequent gene exchanges between and within groups. A selective elimination analysis on the P. hopeiensis population were performed using Fst and π radio and a total of 381 overlapping genes including SAUR72, IAA20, HSFA2, and RKP genes were obtained. These genes were analyzed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) function enrichment. And four KEGG pathways, including lysine degradation, sphingolipid metabolism, other glycan degradation, and betaine biosynthesis were significantly enriched in the P. hopeiensis population. Our study provided information on genetic variation, evolutionary relationships, and gene enrichment in P. hopeiensis population. These data will help reveal the evolutionary history and origin of P. hopeiensis and provide guidelines for subsequent research on the locations of functional genes.https://www.frontiersin.org/articles/10.3389/fpls.2021.668796/fullPyrus hopeiensisSNPswhole genome re-sequencingPCAFst and π ratioKEGG
collection DOAJ
language English
format Article
sources DOAJ
author Yongtan Li
Yongtan Li
Jun Zhang
Jun Zhang
Shijie Wang
Shijie Wang
Yiwen Zhang
Yiwen Zhang
Minsheng Yang
Minsheng Yang
spellingShingle Yongtan Li
Yongtan Li
Jun Zhang
Jun Zhang
Shijie Wang
Shijie Wang
Yiwen Zhang
Yiwen Zhang
Minsheng Yang
Minsheng Yang
The Distribution and Origins of Pyrus hopeiensis-“Wild Plant With Tiny Population” Using Whole Genome Resequencing
Frontiers in Plant Science
Pyrus hopeiensis
SNPs
whole genome re-sequencing
PCA
Fst and π ratio
KEGG
author_facet Yongtan Li
Yongtan Li
Jun Zhang
Jun Zhang
Shijie Wang
Shijie Wang
Yiwen Zhang
Yiwen Zhang
Minsheng Yang
Minsheng Yang
author_sort Yongtan Li
title The Distribution and Origins of Pyrus hopeiensis-“Wild Plant With Tiny Population” Using Whole Genome Resequencing
title_short The Distribution and Origins of Pyrus hopeiensis-“Wild Plant With Tiny Population” Using Whole Genome Resequencing
title_full The Distribution and Origins of Pyrus hopeiensis-“Wild Plant With Tiny Population” Using Whole Genome Resequencing
title_fullStr The Distribution and Origins of Pyrus hopeiensis-“Wild Plant With Tiny Population” Using Whole Genome Resequencing
title_full_unstemmed The Distribution and Origins of Pyrus hopeiensis-“Wild Plant With Tiny Population” Using Whole Genome Resequencing
title_sort distribution and origins of pyrus hopeiensis-“wild plant with tiny population” using whole genome resequencing
publisher Frontiers Media S.A.
series Frontiers in Plant Science
issn 1664-462X
publishDate 2021-06-01
description Pyrus hopeiensis is a valuable but endangered wild resource in the genus Pyrus. It has been listed as one of the 120 wild species with tiny population in China. The specie has been little studied. A preliminary study of propagation modes in P. hopeiensis was performed through seed propagation, hybridization, self-crossing trials, bud grafting, branch grafting, and investigations of natural growth. The results showed that the population size of P. hopeiensis was very small, the distribution range was limited, and the habitat was extremely degraded. In the wild population, natural hybridization and root tiller production were the major modes of propagation. Whole genome re-sequencing of the 23 wild and cultivated accessions from Pyrus species collected was performed using an Illumina HiSeq sequencing platform. The sequencing depth range was 26.56x−44.85x and the average sequencing depth was 32x. Phylogenetic tree and principal component analyses (PCA) based on SNPs showed that the wild Pyrus species, such as PWH06, PWH07, PWH09, PWH10, PWH13, and PWH17, were closely related to both P. hopeiensis HB-1 and P. hopeiensis HB-2. Using these results in combination with morphological characteristics, it speculated that P. hopeiensis populations may form a natural hybrid group with frequent gene exchanges between and within groups. A selective elimination analysis on the P. hopeiensis population were performed using Fst and π radio and a total of 381 overlapping genes including SAUR72, IAA20, HSFA2, and RKP genes were obtained. These genes were analyzed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) function enrichment. And four KEGG pathways, including lysine degradation, sphingolipid metabolism, other glycan degradation, and betaine biosynthesis were significantly enriched in the P. hopeiensis population. Our study provided information on genetic variation, evolutionary relationships, and gene enrichment in P. hopeiensis population. These data will help reveal the evolutionary history and origin of P. hopeiensis and provide guidelines for subsequent research on the locations of functional genes.
topic Pyrus hopeiensis
SNPs
whole genome re-sequencing
PCA
Fst and π ratio
KEGG
url https://www.frontiersin.org/articles/10.3389/fpls.2021.668796/full
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