气候变化领域集成服务门户(CCPortal): Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd

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DOI	10.1111/tpj.12370
	Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd
	Xu, Pei; Xu, Shizhong; Wu, Xiaohua; Tao, Ye; Wang, Baogen; Wang, Sha; Qin, Dehui; Lu, Zhongfu; Li, Guojing
发表日期	2014
ISSN	0960-7412
起始页码	430
结束页码	442
卷号	77 期号:3
英文摘要	Restriction site-associated DNA sequencing (RAD-Seq), a next-generation sequencing-based genome complexity reduction' protocol, has been useful in population genomics in species with a reference genome. However, the application of this protocol to natural populations of genomically underinvestigated species, particularly under low-to-medium sequencing depth, has not been well justified. In this study, a Bayesian method was developed for calling genotypes from an F-2 population of bottle gourd [Lagenaria siceraria (Mol.) Standl.] to construct a high-density genetic map. Low-depth genome shotgun sequencing allowed the assembly of scaffolds/contigs comprising approximately 50% of the estimated genome, of which 922 were anchored for identifying syntenic regions between species. RAD-Seq genotyping of a natural population comprising 80 accessions identified 3226 single nuclear polymorphisms (SNPs), based on which two sub-gene pools were suggested for association with fruit shape. The two sub-gene pools were moderately differentiated, as reflected by the Hudson's F-ST value of 0.14, and they represent regions on LG7 with strikingly elevated F-ST values. Seven-fold reduction in heterozygosity and two times increase in LD (r(2)) were observed in the same region for the round-fruited sub-gene pool. Outlier test suggested the locus LX3405 on LG7 to be a candidate site under selection. Comparative genomic analysis revealed that the cucumber genome region syntenic to the high F-ST island on LG7 harbors an ortholog of the tomato fruit shape gene OVATE. Our results point to a bright future of applying RAD-Seq to population genomic studies for non-model species even under low-to-medium sequencing efforts. The genomic resources provide valuable information for cucurbit genome research.
英文关键词	RAD-Seq; population genomics; shotgun sequencing; Lagenaria siceraria; cucurbit; comparative genomics; fruit shape
WOS研究方向	Plant Sciences
WOS类目	Plant Sciences
来源期刊	PLANT JOURNAL
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/158598
作者单位	Xu, P (corresponding author), Zhejiang Acad Agr Sci, Inst Vegetables, Hangzhou 310021, Zhejiang, Peoples R China.
推荐引用方式 GB/T 7714	Xu, Pei,Xu, Shizhong,Wu, Xiaohua,et al. Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd[J],2014,77(3).
APA	Xu, Pei.,Xu, Shizhong.,Wu, Xiaohua.,Tao, Ye.,Wang, Baogen.,...&Li, Guojing.(2014).Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd.PLANT JOURNAL,77(3).
MLA	Xu, Pei,et al."Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd".PLANT JOURNAL 77.3(2014).