Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in black poplar (Populus nigra L.) inbred lines using the candidate gene approach

被引：0
作者：
Liu X. [1 ]
Lin H. [1 ]
Ding C. [2 ]
Su X. [2 ]
机构：
[1] Fujian Provincial Key Laboratory of Resources and Environment Monitoring and Sustainable Management and Utilization, Sanming University, Sanming, Fujian
[2] Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Beijing
来源：
Scientia Forestalis/Forest Sciences | 2021年 / 49卷 / 129期
基金：
中国国家自然科学基金;
关键词：
Candidate gene; Linkage disequilibrium; Populus nigra; Single nucleotide polymorphism (SNP);
D O I：
10.18671/SCIFOR.V49N129.17
中图分类号：
学科分类号：
摘要：
Populus is an important model organism in forest biology, and Populus nigra is an important tree species in poplar breeding. This research studied the polymorphism pattern of nine candidate genes in regards to N absorption and assimilation in P. nigra. A total of 205 single nucleotide polymorphism (SNP) sites were found in nine genes. The average nucleotide diversity for the sequenced regions were calculated as θw=0.00525 and ΠT=0.00380. The Ka:Ks ratios for all nine genes were lower than 1, indicating the action of purifying selection. Tests of neutrality for each gene revealed that the results reject neutral evolution at PTNRT1.2 and PttAMT1;2. The nucleotide sequences of PTNRT1.2 and PttAMT1;2 likely accepted negative selection, causing a hitchhiking effect. A recombination analysis of the nine candidate genes revealed that the average reorganization event between SNPs in P. nigra r is 0.1951. Linkage disequilibrium (LD) of SNPs in five candidate genes was detected, and the result showed that LD declined rapidly within these gene regions. These outcomes were similar to those determined for other trees, suggesting that wide LD mapping in the whole genome of Populus might be impossible and unnecessary, but LD mapping based on candidate genes could be particularly useful in poplar breeding programs. The results showed that P. nigra was suitable for association analysis with candidate genes and for the development of SNP markers. This article adds knowledge on N absorption and assimilation in poplars. © 2021 University of Sao Paolo. All rights reserved.
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