首页|Phased genomics reveals hidden somatic mutations and provides insight into fruit development in sweet orange

Phased genomics reveals hidden somatic mutations and provides insight into fruit development in sweet orange

扫码查看
原文链接
  • NETL
  • NSTL
  • 万方数据
Although revisiting the discoveries and implications of genetic variations using phased genomics is critical,such efforts are still lacking.Somatic mutations represent a crucial source of genetic diversity for breeding and are especially remarkable in heterozygous perennial and asexual crops.In this study,we focused on a diploid sweet orange(Citrus sinensis)and constructed a haplotype-resolved genome using high fidelity(HiFi)reads,which revealed 10.6％new sequences.Based on the phased genome,we elucidate significant genetic admixtures and haplotype differences.We developed a somatic detection strategy that reveals hidden somatic mutations overlooked in a single reference genome.We generated a phased somatic variation map by combining high-depth whole-genome sequencing(WGS)data from 87 sweet orange somatic varieties.Notably,we found twice as many somatic mutations relative to a single reference genome.Using these hidden somatic mutations,we separated sweet oranges into seven major clades and provide insight into unprecedented genetic mosaicism and strong positive selection.Furthermore,these phased genomics data indicate that genomic heterozygous variations contribute to allele-specific expression during fruit development.By integrating allelic expression differences and somatic mutations,we identified a somatic mutation that induces increases in fruit size.Applications of phased genomics will lead to powerful approaches for discovering genetic variations and uncovering their effects in highly heterozygous plants.Our data provide insight into the hidden somatic mutation landscape in the sweet orange genome,which will facilitate citrus breeding.

Nan Wang、Peng Chen、Yuanyuan Xu、Lingxia Guo、Xianxin Li、Hualin Yi、Robert M.Larkin、Yongfeng Zhou、Xiuxin Deng、Qiang Xu

展开 >

Institute of Horticultural Research,Hunan Academy of Agricultural Sciences,Changsha,China

National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops,Huazhong Agricultural University,Wuhan,China

National Key Laboratory of Tropical Crop Breeding,Shenzhen Branch,Guangdong Laboratory of Lingnan Modem Agriculture,Key Laboratory of Synthetic Biology,Ministry of Agriculture and Rural Affairs,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen,Chi

Yuelu Mountain Laboratory,Changsha,China

Hubei Hongshan Laboratory,Wuhan,China

National Key Laboratory of Tropical Crop Breeding,Shenzhen Branch,Guangdong Laboratory of Lingnan Modem Agriculture,Key Laboratory of Synthetic Biology,Ministry of Agriculture and Rural Affairs,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen,China

National Key Laboratory of Tropical Crop Breeding,Tropical Crops Genetic Resources Institute,Chinese Academy of Tropical Agricultural Sciences,Haikou,China

展开 >

国家重点研发计划国家重点研发计划Agricultural Science and Technology Innovation Funds Project of Hunan ProvinceAgricultural Science and Technology Innovation Funds Project of Hunan Province湖南省自然科学基金

2022YFF10031002019YFD10014002022CX1272023CX712021JJ40308

2024

10.1093/hr/uhad268

园艺研究(英文)

园艺研究(英文)

CSTPCD
ISSN：
年,卷(期)：2024.11(2)
  • 103