Detection of major loci associated with the variation of 18 important agronomic traits between <i>Solanum pimpinellifolium</i> and cultivated tomatoes

Zhang, Shuaibin; Yu, Hong; Wang, Ketao; Zhang, Zheng; Liu, Lei; Xu, Meng; Jiao, Zhicheng; Ren, Li; Liu, Xiyan; Li, Jiayang; Cui, Xia

doi:10.1111/tpj.13952

Cited by 32 publications

(22 citation statements)

References 59 publications

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“…In recent years, whole-genome re-sequencing technology has been widely used in population genetic analysis [24][25][26]. The high-throughput genotyping platform of SNP markers has significantly driven the process of genetic mapping and QTL identification [27][28][29]. Compared with the low density of traditional molecular markers, SNP markers significantly improve the genome coverage and QTL mapping accuracy.…”

Section: Introductionmentioning

confidence: 99%

Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton

Zhu

Wang

et al. 2020

BMC Genomics

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Background: The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization. Results: In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions: This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.

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Section: Introductionmentioning

confidence: 99%

Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton

Zhu

Wang

et al. 2020

BMC Genomics

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“…These sources of diversity, especially in the wild species, provide a reservoir of genetic variation for future crop improvement [22][23][24]. For example, introgression from related wild species into domesticated tomato has been used to improve agronomic performance such as abiotic tolerance [25][26][27][28]. Similarly, a gene from a wild relative of bread wheat has been shown to confer resistance to one of the most destructive stem rust pathogen races, Ug99 [29].…”

Section: Introductionmentioning

confidence: 99%

Benchmarking Variant Identification Tools for Plant Diversity Discovery

Heffelfinger

Zhao

et al. 2019

Preprint

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Background The ability to accurately and comprehensively identify genomic variations is critical for plant studies utilizing high-throughput sequencing. Most bioinformatics tools for processing next-generation sequencing data were originally developed and tested in human studies, raising questions as to their efficacy for plant research. A detailed evaluation of the entire variant calling pipeline, including alignment, variant calling, variant filtering, and imputation was performed on different programs using both simulated and real plant genomic datasets. Results A comparison of SOAP2, Bowtie2, and BWA-MEM found that BWA-MEM was consistently able to align the most reads with high accuracy, whereas Bowtie2 had the highest overall accuracy. Comparative results of GATK HaplotypCaller versus SAMtools mpileup indicated that the choice of variant caller affected precision and recall differentially depending on the levels of diversity, sequence coverage and genome complexity. A cross-reference experiment of S. lycopersicum and S. pennellii reference genomes revealed the inadequacy of single reference genome for variant discovery that includes distantly-related plant individuals. Machine-learning-based variant filtering strategy outperformed the traditional hard-cutoff strategy resulting in higher number of true positive variants and fewer false positive variants. The 2-step imputation which utilized a set of high-confidence SNPs as the reference panel showed up to 60% higher accuracy than direct LD-based imputation method. Conclusions Programs in the variant discovery pipeline have different performance on plant genomic dataset. Choice of the programs is subjected to the goal of the study and available resources. This study serves as an important guiding information for plant biologists utilizing next-generation sequencing data for diversity characterization and crop improvement.

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“…In this study, we identi ed a total of 239 signi cant signals corresponding to 129 genome loci associated with the 27 assessed agronomic traits. Of these, many signi cant signals for organ size, organ number and organ location traits were colocated with candidate genes identi ed by a previous linkage analysis 28 ( Supplementary Tables 4 and 5). In addition, many novel candidate genes were also identi ed by our GWAS.…”

Section: Discussionmentioning

confidence: 99%

“…Genome-wide association study (GWAS) is an effective approach to investigate the genetic architecture of complex agronomic traits in crops 23,24,25,26,27 . In tomato, using bi-parental populations, several loci for important agronomic traits have been identi ed 28 . Recently, GWAS has been employed to explore genetic loci associated with 15 agronomic traits in 163 tomato accessions 29 .…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study reveals the genetic architecture of 27 yield-related traits in tomato

Wang

et al. 2020

Preprint

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Tomato (Solanum lycopersicum) is a highly valuable vegetable crop and yield is one of the most important traits. Uncovering the genetic architecture of yield-related traits in tomato is critical for the management of vegetative and reproductive development, thereby enhancing yield. Here we perform a comprehensive genome-wide association study for 27 yield-related traits in tomato. A total of 239 significant associations corresponding to 129 loci, harboring many reported and novel genes related to vegetative and reproductive development, were identified, and these loci explained an average of ~8.8% of the phenotypic variance. A total of 51 loci associated with 25 traits have been under selection, especially during tomato improvement. Furthermore, a candidate gene, SlALMT15 that encodes an aluminum-activated malate transporter, was functionally characterized and shown to act as a pivotal regulator of leaf stomata formation through increasing photosynthesis and drought resistance. This study provides valuable information for tomato genetic research and breeding.

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Detection of major loci associated with the variation of 18 important agronomic traits between Solanum pimpinellifolium and cultivated tomatoes

Cited by 32 publications

References 59 publications

Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton

Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton

Benchmarking Variant Identification Tools for Plant Diversity Discovery

Genome-wide association study reveals the genetic architecture of 27 yield-related traits in tomato

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