Estimation of QTL heritability based on pooled sequencing data

被引：12
作者：
Tang, Weiqi [1 ,2 ]
Huang, Likun [1 ,2 ]
Bu, Suhong [1 ,2 ]
Zhang, Xuzhang [1 ,2 ]
Wu, Weiren [1 ,2 ]
机构：
[1] Fujian Agr & Forestry Univ, Coll Life Sci, Key Lab Genet Breeding & Multiple Utilizat Crops, Minist Educ, Fuzhou 350002, Fujian, Peoples R China
[2] Fujian Agr & Forestry Univ, Fujian Key Lab Crop Breeding Design, Fuzhou 350002, Fujian, Peoples R China
来源：
BIOINFORMATICS | 2018年 / 34卷 / 06期
关键词：
BULKED SEGREGANT ANALYSIS; GENETIC ARCHITECTURE; GENOMIC REGIONS; CANDIDATE GENES; COMPLEX TRAIT; IDENTIFICATION; SEQ; TOLERANCE; DISEASE; WEIGHT;
D O I：
10.1093/bioinformatics/btx703
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
Motivation: Bulked segregant analysis combined with next generation sequencing has proven to be a simple and efficient approach for fast mapping of quantitative trait loci (QTLs). However, how to estimate the proportion of phenotypic variance explained by a QTL (or termed QTL heritability) in such pooled QTL mapping is an unsolved problem. Results: In this paper, we propose a method called PQHE to estimate QTL heritability using pooled sequencing data obtained under different experimental designs. Simulation studies indicated that our method is correct and feasible. Four practical examples from rice and yeast are demonstrated, each representing a different situation.
引用
收藏
页码：978 / 984
页数：7
相关论文
共 50 条
  • [21] Fast and accurate haplotype frequency estimation for large haplotype vectors from pooled DNA data
    Iliadis, Alexandros
    Anastassiou, Dimitris
    Wang, Xiaodong
    BMC GENETICS, 2012, 13
  • [22] Normalization, testing, and false discovery rate estimation for RNA-sequencing data
    Li, Jun
    Witten, Daniela M.
    Johnstone, Iain M.
    Tibshirani, Robert
    BIOSTATISTICS, 2012, 13 (03) : 523 - 538
  • [23] CoNVEX: copy number variation estimation in exome sequencing data using HMM
    Amarasinghe, Kaushalya C.
    Li, Jason
    Halgamuge, Saman K.
    BMC BIOINFORMATICS, 2013, 14
  • [24] QTL mapping of drought tolerance traits in soybean with SLAF sequencing
    Ren, Honglei
    Han, Jianan
    Wang, Xingrong
    Zhang, Bo
    Yu, Lili
    Gao, Huawei
    Hong, Huilong
    Sun, Rujian
    Tian, Yu
    Qi, Xusheng
    Liu, Zhangxiong
    Wu, Xiaoxia
    Qiu, Li-Juan
    CROP JOURNAL, 2020, 8 (06): : 977 - 989
  • [25] Typing methods based on whole genome sequencing data
    Uelze, Laura
    Gruetzke, Josephine
    Borowiak, Maria
    Hammerl, Jens Andre
    Juraschek, Katharina
    Deneke, Carlus
    Tausch, Simon H.
    Malorny, Burkhard
    ONE HEALTH OUTLOOK, 2020, 2 (01):
  • [26] Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis
    Wei, Qing-zhen
    Fu, Wen-yuan
    Wang, Yun-zhu
    Qin, Xiao-dong
    Wang, Jing
    Li, Ji
    Lou, Qun-feng
    Chen, Jin-feng
    SCIENTIFIC REPORTS, 2016, 6
  • [27] Statistical methods for SNP heritability estimation and partition: A review
    Zhu, Huanhuan
    Zhou, Xiang
    COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 2020, 18 : 1557 - 1568
  • [28] Biomarker screening in preeclampsia: an RNA-sequencing approach based on data from multiple studies
    Rezk, Marlene
    Grasegger, Linda
    Brandstetter, Nina
    Pol-Edern, Le Renard
    Stelzl, Patrick
    Oppelt, Peter
    Arbeithuber, Barbara
    JOURNAL OF HYPERTENSION, 2022, 40 (10) : 2022 - 2036
  • [29] High-density genetic linkage map construction and cane cold hardiness QTL mapping for Vitis based on restriction site-associated DNA sequencing
    Su, Kai
    Xing, Huiyang
    Guo, Yinshan
    Zhao, Fangyuan
    Liu, Zhendong
    Li, Kun
    Li, Yuanyuan
    Guo, Xiuwu
    BMC GENOMICS, 2020, 21 (01)
  • [30] ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
    Margarido, Gabriel R. A.
    Heckerman, David
    PLOS COMPUTATIONAL BIOLOGY, 2015, 11 (04)
12345