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

机构：[1] Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, China; [2] National Forestry and Grassland Engineering Technology Research Center of Exotic Pine Cultivation, Hangzhou, 311400, China; [3] Ume? Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Ume?, Sweden; [4] CSIRO National Collection Research Australia, Black Mountain Laboratory, Canberra, Australia; [5] Beijing Victory Time Company Co., Ltd, Beijing, 102221, China; [6] State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China; [7] Tianjin GenoAgri Breeding Company Co., Ltd, Tianjin, 120111, 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)

语种：英文

外文关键词：DNA sequences - Gene encoding - Genome - Principal component analysis - Transcription

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. ? 2024 Elsevier B.V.