Journal ArticleDOI
Genome-wide association analysis of salt tolerance QTLs with SNP markers in maize (Zea mays L.).
Xie Yonghong,Yan Feng,Qi Chen,Feike Zhao,Shuijuan Zhou,Ying Ding,Xianliang Song,Li Ping,Baohua Wang +8 more
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TLDR
Genome-wide association study (GWAS) was carried out to identify the significant single nucleotide polymorphisms (SNPs) which were associated with maize salt tolerance, which will be of special value in molecular breeding of salt-tolerant maize.Abstract:
Salt-tolerant breeding of maize has great significance to the development and utilization of saline–alkaline soil and the maintenance of grain security. Genome-wide association study (GWAS) has been widely used in maize genetics and breeding. To discover new salt-tolerant genes in maize by association analysis, which can provide technical supports for the innovation and genetic improvement of salt-tolerant germplasm resources in maize. Totally 150 maize inbred lines were genotyped with a high-density chip. GWAS was carried out to identify the significant single nucleotide polymorphisms (SNPs) which were associated with maize salt tolerance. Totally 34,972 SNPs with high quality and diversity were selected from 56,110 SNP markers, which were distributed on 10 chromosomes of maize. The GLM algorithm in TASSEL5.2 was used to analyze the five traits related to salt tolerance. Using a strict LOD threshold of 4.5, totally 7 SNP loci were identified, which were significantly correlated with plant height change rate and fresh weight change rate. The high density fingerprints of 150 inbred lines were clustered by TASSEL5.2 software to construct genetic clustering map to estimate the genetic distance and the subgroups. The 150 maize inbred lines were divided into two groups: SS group and NSS group, and the SNP loci of the salt-tolerant index showed difference in chromosome distribution. Based on previous studies, we screened 8 candidate genes for salt tolerance in maize and four of them were further validated by real-time quantitative PCR. Totally 7 SNP loci and 8 candidate genes related to salt tolerance in maize were identified, which will be of special value in molecular breeding of salt-tolerant maize.read more
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Journal ArticleDOI
Molecular dissection of maize seedling salt tolerance using a genome-wide association analysis method.
Meijie Luo,Yunxia Zhang,Jingna Li,Panpan Zhang,Kuan Chen,Wei Song,Xiaqing Wang,Yang Jinxiao,Xiaoduo Lu,Lu Baishan,Yanxin Zhao,Jiuran Zhao +11 more
TL;DR: In this paper, a genome-wide association study was performed on 348 maize inbred lines under normal and salt stress conditions using 557 894 single nucleotide polymorphisms (SNPs).
Clone and sequence analysis of the specific mitochondrial genes Cox II and atp6 related to cytoplasmic male sterile in pepper.
TL;DR: The result suggested a close relationship of pepper CMS with the variation in DNA sequence of CoxⅡ and atp6 gene in CMS line.
Journal ArticleDOI
Characterization and genetic dissection of maize ear leaf midrib acquired by 3D digital technology
Sheng Wu,Jinglu Wang,Yanxin Zhao,Weiliang Wen,Ying Zhang,Xianju Lu,Chuanyu Wang,Kai Liu,Bo Chen,Xinyu Guo,Chunjiang Zhao +10 more
TL;DR: In this paper , the ear leaf midrib of maize was characterized using 3D digitization technology and 13 phenotypic traits were firstly proposed for featuring plant leaf spatial structure, which can be divided into four groups, Group I, -II, -III and -IV.
Journal ArticleDOI
Co-expression pan-network reveals genes involved in complex traits within maize pan-genome
TL;DR: In this article , a large collection of gene co-expression networks and more than 2 million co-expressing gene pairs were identified in the GWAS-driven pan-network which contains all the gene-pairs in individual genomes of the nested association mapping (NAM) population.
References
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TL;DR: STRUCTURE HARVESTER is presented, a web-based program for collating results generated by the program STRUCTURE, which provides a fast way to assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of the number of genetic groups that best fit the data.
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The interplay between habitat availability and population differentiation
Yvonne I. Verkuil,Theunis Piersma,Joop Jukema,Leo Zwarts,Allan J. Baker,Jos C.E.W. Hooijmeijer +5 more
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Sequencing technologies-the next generation
TL;DR: A technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments is presented.
Journal ArticleDOI
TASSEL: software for association mapping of complex traits in diverse samples
Peter J. Bradbury,Zhiwu Zhang,Dallas E. Kroon,Terry M. Casstevens,Yogesh Ramdoss,Edward S. Buckler +5 more
TL;DR: TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear model and mixed linear model approaches for controlling population and family structure and allows for linkage disequilibrium statistics to be calculated and visualized graphically.