Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops

Cao, Ke; Zheng, Zhijun; Wang, Lirong; Liu, Xin; Zhu, Guoqiang; Fang, Weichao; Cheng, Shifeng; Zeng, Peng; Chen, Chang Wen; Wang, Xinwei; Xie, Min; Zhong, Xiao Bo; Wang, Xiaoli; Zhao, Pei; Bian, Chao; Zhu, Yuxia; Zhang, Jiahui; Guo-sheng, MA; Chen, Chengxuan; Li, Yanjun; Hao, Fengge; Li, Yong; Huang, Guodong; Li, Yuxiang; Li, Haiyan; Guo, Jian; Xu, Xun; Wang, Jun

doi:10.1186/s13059-014-0415-1

Cited by 126 publications

(153 citation statements)

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“…CDRs were selected based on an ROD along with F st method (Cao et al 2014;Xu et al 2012b). CDRs were selected based on an ROD along with F st method (Cao et al 2014;Xu et al 2012b).…”

Section: Identification Of Candidate Domestication Regions and Expresmentioning

confidence: 99%

“…Selection during domestication frequently leads to a differential loss of genetic diversity at specific genes in targeted genomic regions that control the trait subject to selection. A combination of ROD and F st measures has been used to screen the candidate regions under selection, because the genomic region with higher ROD value gave higher F st value (Cao et al 2014). Thus, searching for genetic bottlenecks associated with losses in variation enables the identification of specific genes or mutations that underlie domestication-related traits.…”

Section: Introductionmentioning

confidence: 99%

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Identification of candidate domestication regions in the radish genome based on high-depth resequencing analysis of 17 genotypes

Kim

Jeong

et al. 2016

Theor Appl Genet

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This study provides high-quality variation data of diverse radish genotypes. Genome-wide SNP comparison along with RNA-seq analysis identified candidate genes related to domestication that have potential as trait-related markers for genetics and breeding of radish. Radish (Raphanus sativus L.) is an annual root vegetable crop that also encompasses diverse wild species. Radish has a long history of domestication, but the origins and selective sweep of cultivated radishes remain controversial. Here, we present comprehensive whole-genome resequencing analysis of radish to explore genomic variation between the radish genotypes and to identify genetic bottlenecks due to domestication in Asian cultivars. High-depth resequencing and multi-sample genotyping analysis of ten cultivated and seven wild accessions obtained 4.0 million high-quality homozygous single-nucleotide polymorphisms (SNPs)/insertions or deletions. Variation analysis revealed that Asian cultivated radish types are closely related to wild Asian accessions, but are distinct from European/American cultivated radishes, supporting the notion that Asian cultivars were domesticated from wild Asian genotypes. SNP comparison between Asian genotypes identified 153 candidate domestication regions (CDRs) containing 512 genes. Network analysis of the genes in CDRs functioning in plant signaling pathways and biochemical processes identified group of genes related to root architecture, cell wall, sugar metabolism, and glucosinolate biosynthesis. Expression profiling of the genes during root development suggested that domestication-related selective advantages included a main taproot with few branched lateral roots, reduced cell wall rigidity and favorable taste. Overall, this study provides evolutionary insights into domestication-related genetic selection in radish as well as identification of gene candidates with the potential to act as trait-related markers for background selection of elite lines in molecular breeding.

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“…CDRs were selected based on an ROD along with F st method (Cao et al 2014;Xu et al 2012b). CDRs were selected based on an ROD along with F st method (Cao et al 2014;Xu et al 2012b).…”

Section: Identification Of Candidate Domestication Regions and Expresmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification of candidate domestication regions in the radish genome based on high-depth resequencing analysis of 17 genotypes

Kim

Jeong

et al. 2016

Theor Appl Genet

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“…The sequencing data from the 84 accessions have been submitted to the Sequence Read Archive [66] under accession number SRA073649.…”

Section: Data Accessmentioning

confidence: 99%

Comparative population genomics reveals the domestication history of the peach,

Cao¹,

Zheng²,

Wang³

et al. 2014

Genome Biol

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Background: Recently, many studies utilizing next generation sequencing have investigated plant evolution and domestication in annual crops. Peach, Prunus persica, is a typical perennial fruit crop that has ornamental and edible varieties. Unlike other fruit crops, cultivated peach includes a large number of phenotypes but few polymorphisms. In this study, we explore the genetic basis of domestication in peach and the influence of humans on its evolution. Results: We perform large-scale resequencing of 10 wild and 74 cultivated peach varieties, including 9 ornamental, 23 breeding, and 42 landrace lines. We identify 4.6 million SNPs, a large number of which could explain the phenotypic variation in cultivated peach. Population analysis shows a single domestication event, the speciation of P. persica from wild peach. Ornamental and edible peach both belong to P. persica, along with another geographically separated subgroup, Prunus ferganensis. We identify 147 and 262 genes under edible and ornamental selection, respectively. Some of these genes are associated with important biological features. We perform a population heterozygosity analysis in different plants that indicates that free recombination effects could affect domestication history. By applying artificial selection during the domestication of the peach and facilitating its asexual propagation, humans have caused a sharp decline of the heterozygote ratio of SNPs.

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“…Phylogenetic analysis has been applied to many species, for example, Brassica oleracea and Arabidopsis thaliana (Town et al, 2006), lettuce lines (Kwon et al, 2013), peach varieties (Cao et al, 2014), wheat (Petersen et al, 2006) and many more. Substantial variation in pairwise SNP numbers between varieties was observed in this study (Table 3- and Australian Premium White (H45 in Western Australia and Victoria, Drysdale in Victoria).…”

Section: Discussionmentioning

confidence: 99%

Genome diversity in Triticum aestivum

Lai¹

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The aims of this PhD research are to identify and characterise genome diversity in Triticum aestivum (bread wheat).This research will establish a process for the identification of large numbers of single nucleotide polymorphisms (SNPs) and other genetic variations in Triticum aestivum.Single nucleotide polymorphisms (SNPs) are the most abundant type of molecular genetic marker and can be used for producing high-resolution genetic maps, marker-trait association studies and marker assisted breeding. Large polyploid genomes, such as wheat, present a challenge for SNP discovery due to the potential presence of multiple homoeologues for each gene.AutoSNPdb has been successfully applied to identify SNPs from Sanger sequence data for several species, including barley, rice and Brassica, but the volume of data required to accurately call SNPs in the complex genome of wheat has prevented its application to this important crop. DNA sequencing technology has been revolutionised by the introduction of next generation sequencing, and it is now possible to generate several million sequence reads in a timely and cost effective manner.Wheat transcriptome sequence data has been generated using Roche 454 Life Sciences technology. This data has been applied for SNP discovery using a modified autoSNPdb method, which integrates SNP and gene annotation information with a graphical viewer. A total of 4,694,141 sequence reads from three bread wheat varieties were assembled to identify a total of 38,928 candidate SNPs. Each SNP is within an assembly complete with annotation, enabling the selection of polymorphism within genes of interest.The discovery of large numbers of genomic SNPs across 16 Australian diverse bread wheat varieties has been completed using a novel algorithm SGSautoSNP. More than 10x whole genome shotgun Illumina paired read sequence data was generated through a bioplatforms collaboration and the data mapped to the draft assemblies of chromosomes ii 7A, 7B and 7D. Over 4 million inter-varietal SNPs were identified. SNP density varied along the lengths chromosome syntenic builds as well as between genomes.SNP density analysis and SNP transition/transversion ratio analysis provide insights into the evolution and breeding history of this important crop. Both the SNP density and SNP transition/transversion ratios across the D genome are significantly lower than across the A and B genomes. This difference reflects the evolutionary history of this crop. In addition, genes within low SNP density regions may have been selected during domestication and breeding. Furthermore, this SNP resource permits the application of high resolution skim based genotyping by sequencing (GBS), trait association and analysis of structural variation in populations.An integrated database and portal for wheat genome resource, WheatGenome.info, has been established and published online. This portal provides a variety of web-based systems hosting wheat genome and genomic data, including genomic SNPs, to support wheat research and crop improve...

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Comparative population genomics reveals the domestication history of the peach, Prunus persica, and human influences on perennial fruit crops

Cited by 126 publications

References 58 publications

Identification of candidate domestication regions in the radish genome based on high-depth resequencing analysis of 17 genotypes

Identification of candidate domestication regions in the radish genome based on high-depth resequencing analysis of 17 genotypes

Comparative population genomics reveals the domestication history of the peach,

Genome diversity in Triticum aestivum

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