文献类型：期刊文献

英文题名：Development of 51 K liquid-phased probe array for Loblolly and Slash pines and its application to GWAS of Slash pine breeding population

作者：Diao, Shu[1,2] Ding, Xianyin[1,2] Luan, Qifu[1,2] Chen, Zhi-Qiang[3] Wu, Harry X.[2,3,4] Li, Xinchun[5,7] Zhang, Yini[1] Sun, Jiaming[1] Wu, Yadi[1] Zou, Long-Hai[6] Jiang, Jingmin[1,2]

第一作者：Diao, Shu;刁姝

通信作者：Luan, QF[1]

机构：[1]Chinese Acad Forestry, Res Inst Subtrop Forestry, Hangzhou 311400, Peoples R China;[2]Natl Forestry & Grassland Engn Technol Res Ctr Exo, Hangzhou 311400, Peoples R China;[3]Swedish Univ Agr Sci, Umea Plant Sci Ctr, Dept Forest Genet & Plant Physiol, Umea, Sweden;[4]CSIRO Natl Collect Res Australia, Black Mt Lab, Canberra, Australia;[5]Beijing Victory Time Co Co Ltd, Beijing 102221, Peoples R China;[6]Zhejiang A&F Univ, Bamboo Ind Inst, State Key Lab Subtrop Silviculture, Hangzhou 311300, Peoples R China;[7]Tianjin GenoAgri Breeding Co Co Ltd, Tianjin 120111, Peoples R China

年份：2024

卷号：216

外文期刊名：INDUSTRIAL CROPS AND PRODUCTS

收录：;EI(收录号：20242116117236);Scopus(收录号：2-s2.0-85193437092);WOS:【SCI-EXPANDED(收录号:WOS:001321114900001)】；

基金：This research was funded by the Science and Technology Innovation 2030 Program, Ministry of Science and Technology, People's Republic of China (2023ZD04059) and the National Key Research and Development Program of Ministry of Science and Technology of the People's Republic of China (2022YFD2200023-2) .

语种：英文

外文关键词：In-solution probe; Genotyping by target sequencing; SNPs; Genetic variation; Candidate gene

摘要：Loblolly pine (Pinus taeda) and Slash pine (Pinus elliottii) are important economically and ecologically tree species worldwide. To implement genomic based breeding strategy, genotyping large number of samples is needed. However, huge and complex pines genome make it difficult to obtain abundant and cost-effectively markers. In this study, we designed a SNP array containing 51 K liquid-phased probes based on the published SNPs and probes of the two species, novel Slash pine-specific long-read transcript, and SNPs obtained from a double digest Restriction-Site Associated DNA sequencing (ddRADseq). We performed targeted capture sequencing using the developed SNP array on three pine species of Loblolly, Slash, and Caribbean pine (Pinus caribaea). The probe capture had an efficiency of 68.26% on average. Principal Component Analysis (PCA), phylogenetic analysis, and genetic structure analysis of 28,670 SNPs genotyped for the three pine species demonstrated the transferability of the SNP array for the three pines. Furthermore, we genotyped 221 range-wide Slash pine genotypes, analyzed their genetic diversity and performed a genome-wide association study (GWAS). We identified 95 SNPs significantly associated with growth and wood quality traits of Slash pine. We have identified potential roles of the MYB2 and MYB46 transcription factors in regulating cell cycle and differentiation in Slash pine, while also suggesting that AP2/ERF and Glycosyl hydrolase may play significant roles in wood formation processes. This new SNP array can be widely applied in future molecular breeding research of conifers.