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Genome Biol. 2018 Jun 11;19(1):77. doi: 10.1186/s13059-018-1452-y.

Diversification and independent domestication of Asian and European pears.

Author information

1
Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
2
Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang Fruit Tree Research Institute, Shijiazhuang, 050061, China.
3
BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
4
University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
5
Plant Pathology and Plant-Microbe Section, Cornell University, Geneva, NY, 14853, USA.
6
USDA-ARS, Boyce Thompson Institute, Ithaca, NY, 14853, USA.
7
Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
8
USDA-ARS National Clonal Germplasm Repository, Corvallis, OR, 97333, USA.
9
The New Zealand Institute for Plant & Food Research Limited, Auckland, New Zealand.
10
James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China.
11
Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China. slzhang@njau.edu.cn.

Abstract

BACKGROUND:

Pear (Pyrus) is a globally grown fruit, with thousands of cultivars in five domesticated species and dozens of wild species. However, little is known about the evolutionary history of these pear species and what has contributed to the distinct phenotypic traits between Asian pears and European pears.

RESULTS:

We report the genome resequencing of 113 pear accessions from worldwide collections, representing both cultivated and wild pear species. Based on 18,302,883 identified SNPs, we conduct phylogenetics, population structure, gene flow, and selective sweep analyses. Furthermore, we propose a model for the divergence, dissemination, and independent domestication of Asian and European pears in which pear, after originating in southwest China and then being disseminated throughout central Asia, has eventually spread to western Asia, and then on to Europe. We find evidence for rapid evolution and balancing selection for S-RNase genes that have contributed to the maintenance of self-incompatibility, thus promoting outcrossing and accounting for pear genome diversity across the Eurasian continent. In addition, separate selective sweep signatures between Asian pears and European pears, combined with co-localized QTLs and differentially expressed genes, underline distinct phenotypic fruit traits, including flesh texture, sugar, acidity, aroma, and stone cells.

CONCLUSIONS:

This study provides further clarification of the evolutionary history of pear along with independent domestication of Asian and European pears. Furthermore, it provides substantive and valuable genomic resources that will significantly advance pear improvement and molecular breeding efforts.

KEYWORDS:

Fruit-related traits; Independent domestication; Origin and evolution; Pear (Pyrus); Re-sequencing genomes; Self-incompatibility

PMID:
29890997
PMCID:
PMC5996476
DOI:
10.1186/s13059-018-1452-y
[Indexed for MEDLINE]
Free PMC Article

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