Identification of favorable haplotypes/alleles and candidate genes for three plant architecture-related traits via a restricted two-stage multilocus genome-wide association study in upland cotton

生物 遗传学 全基因组关联研究 连锁不平衡 等位基因 基因座(遗传学) 单核苷酸多态性 遗传建筑学 单倍型 人口 数量性状位点 遗传关联 候选基因 关联映射 基因 基因型 人口学 社会学
作者
Caixiang Wang,Qi Ma,Xiaoyu Xie,Xianliang Zhang,Delong Yang,Junji Su,Xiongfeng Ma,Hai Lin
出处
期刊:Industrial Crops and Products [Elsevier BV]
卷期号:177: 114458-114458 被引量:10
标识
DOI:10.1016/j.indcrop.2021.114458
摘要

Plant architecture-related traits are extremely crucial for cotton plants and are closely linked to their ability to adapt to reasonably close planting and to their suitability for mechanized harvesting. However, the genetic basis for cotton plant architecture-related traits remains poorly understood. To identify favorable haplotypes/alleles (FHs/FAs) and candidate genes for target traits, we performed a restricted two-stage multilocus genome-wide association study (RTM-GWAS) using a natural population consisting of 315 upland cotton accessions and 9244 single-nucleotide polymorphism linkage disequilibrium blocks (SNPLDBs), which were explored and established using the specific-locus amplified fragment sequencing (SLAF-seq) technique. Totals of 68, 34 and 55 significant SNPLDB loci associated with the plant height (PH), fruit branch angle (FBA) and fruit branch length (FBL), respectively, were identified via the RTM-GWAS method. We then estimated the allele effects of the significant loci associated with the target traits and further generated SNPLDB allele matrices to provide a brief inheritance constitution of the population. Among the significant SNPLDB associations, five involved in four major loci (LDB_1_21982826, LDB_9_51578589_51578819, LDB_16_37952328 and LDB_19_52309050_52309284) for the PH or FBL were concurrently detected in a multiple-environment combined model and in at least one single-environment model. A comparison of FHs/FAs frequencies for the four major SNPLDB loci revealed that the frequencies of FHs or FAs that were hidden in short and compact cotton accessions were much higher than those in tall and noncompact cotton accessions. We also observed that cotton accessions from the northern super-early-maturation region (NSER) had relatively short and compact plants compared with those from the Yangtze River region (YZRR) and northwestern inland region (NIR), and the high FA frequencies of the four major SNPLDB loci were consistent with the relatively short and compact plant architecture in five different geographic regions. In the neighboring genome fragments of the four major SNPLDB loci, ultimately, the five candidate genes that were highly expressed during the early stages of the growth and were responsible for cotton PH and FBL through the auxin signaling pathway were explored by RNA-seq data and bioinformatics analysis. This study identified FHs/FAs and candidate genes for PH and FBL, which could provide key insights into the genetic basis for the plant architecture of upland cotton and could promote the breeding of new cotton varieties with ideal plant architecture suitable for mechanized harvesting.
最长约 10秒,即可获得该文献文件

科研通智能强力驱动
Strongly Powered by AbleSci AI
更新
PDF的下载单位、IP信息已删除 (2025-6-4)

科研通是完全免费的文献互助平台,具备全网最快的应助速度,最高的求助完成率。 对每一个文献求助,科研通都将尽心尽力,给求助人一个满意的交代。
实时播报
科研通AI2S应助感动黄豆采纳,获得10
3秒前
7秒前
8秒前
11秒前
Fengliguantou发布了新的文献求助10
11秒前
猪猪hero发布了新的文献求助10
13秒前
Winner发布了新的文献求助10
15秒前
隐形曼青应助科研通管家采纳,获得10
15秒前
领导范儿应助科研通管家采纳,获得10
15秒前
Lucas应助科研通管家采纳,获得30
16秒前
16秒前
圆锥香蕉应助科研通管家采纳,获得20
16秒前
科研通AI2S应助科研通管家采纳,获得10
16秒前
科研通AI2S应助科研通管家采纳,获得10
16秒前
科目三应助科研通管家采纳,获得10
16秒前
充电宝应助科研通管家采纳,获得10
16秒前
脑洞疼应助科研通管家采纳,获得10
16秒前
科研通AI5应助科研通管家采纳,获得10
16秒前
852应助科研通管家采纳,获得10
16秒前
科研通AI2S应助科研通管家采纳,获得10
16秒前
科研通AI2S应助科研通管家采纳,获得10
16秒前
情怀应助科研通管家采纳,获得10
17秒前
17秒前
感动黄豆发布了新的文献求助10
17秒前
20秒前
搞怪冷风完成签到,获得积分10
21秒前
lucky完成签到,获得积分10
21秒前
量子星尘发布了新的文献求助10
22秒前
24秒前
科目三应助战斗暴龙兽采纳,获得10
28秒前
28秒前
28秒前
29秒前
29秒前
32秒前
故意的靳发布了新的文献求助50
33秒前
111111完成签到,获得积分10
33秒前
郭小宝发布了新的文献求助20
35秒前
youwenjing11发布了新的文献求助10
36秒前
hello发布了新的文献求助10
36秒前
高分求助中
A new approach to the extrapolation of accelerated life test data 1000
ACSM’s Guidelines for Exercise Testing and Prescription, 12th edition 500
‘Unruly’ Children: Historical Fieldnotes and Learning Morality in a Taiwan Village (New Departures in Anthropology) 400
Indomethacinのヒトにおける経皮吸収 400
Phylogenetic study of the order Polydesmida (Myriapoda: Diplopoda) 370
基于可调谐半导体激光吸收光谱技术泄漏气体检测系统的研究 350
Robot-supported joining of reinforcement textiles with one-sided sewing heads 320
热门求助领域 (近24小时)
化学 材料科学 医学 生物 工程类 有机化学 生物化学 物理 内科学 纳米技术 计算机科学 化学工程 复合材料 遗传学 基因 物理化学 催化作用 冶金 细胞生物学 免疫学
热门帖子
关注 科研通微信公众号,转发送积分 3989115
求助须知:如何正确求助?哪些是违规求助? 3531367
关于积分的说明 11253688
捐赠科研通 3269986
什么是DOI,文献DOI怎么找? 1804868
邀请新用户注册赠送积分活动 882078
科研通“疑难数据库(出版商)”最低求助积分说明 809105