Identification of QTL for resistance to leaf blast in foxtail millet by genome re-sequencing analysis

Tian, Bohong; Zhang, Lixin; Li, Yanli; Wu, Peipei; Wang, Wei; Zhang, Yue; Li, Hongjie

doi:10.1007/s00122-020-03730-w

Cited by 17 publications

(8 citation statements)

References 23 publications

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“…Nuclear DNA markers, such as microsatellites (SSRs) [ 12 ], randomly amplified polymorphic DNA markers [ 13 ], and chloroplast DNA [ 14 ] have been used to detect introgression across species. With advancements in genomic studies, our understanding of the ecological, genetic, and genomic factors underlying the diverse outcomes of interspecific introgression in hybrid zones is increasing [ 15 – 17 ].…”

Section: Introductionmentioning

confidence: 99%

Hybridization and introgression in sympatric and allopatric populations of four oak species

Wei

El‐Kassaby

et al. 2021

BMC Plant Biol

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Background Hybridization and introgression are vital sources of novel genetic variation driving diversification during reticulated evolution. Quercus is an important model clade, having extraordinary diverse and abundant members in the Northern hemisphere, that are used to studying the introgression of species boundaries and adaptive processes. China is the second-largest distribution center of Quercus, but there are limited studies on introgressive hybridization. Results Here, we screened 17 co-dominant nuclear microsatellite markers to investigate the hybridization and introgression of four oaks (Quercus acutissima, Quercus variabilis, Quercus fabri, and Quercus serrata) in 10 populations. We identified 361 alleles in the four-oak species across 17 loci, and all loci were characterized by high genetic variability (HE = 0.844–0.944) and moderate differentiation (FST = 0.037–0.156) levels. A population differentiation analysis revealed the following: allopatric homologous (FST = 0.064) < sympatric heterogeneous (FST = 0.071) < allopatric heterogeneous (FST = 0.084). A Bayesian admixture analysis determined four types of hybrids (Q. acutissima × Q. variabilis, Q. fabri × Q. serrata, Q. acutissima × Q. fabri, and Q. acutissima × Q. variabilis × Q. fabri) and their asymmetric introgression. Our results revealed that interspecific hybridization is commonly observed within the section Quercus, with members having tendency to hybridize. Conclusions Our study determined the basic hybridization and introgression states among the studied four oak species and extended our understanding of the evolutionary role of hybridization. The results provide useful theoretical data for formulating conservation strategies.

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Section: Introductionmentioning

confidence: 99%

Hybridization and introgression in sympatric and allopatric populations of four oak species

Wei

El‐Kassaby

et al. 2021

BMC Plant Biol

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“…A large number of molecular markers have been developed and utilized, including single-nucleotide polymorphisms (SNPs), indels, structural variants, simple-sequence repeats (SSRs), and Expressed Sequence Tag-SSRs [13][14][15][16][17]. The rapid development of sequencing technology in recent years allowed large-scale wholegenome sequencing becoming possible, and further facilitate numbers of quantitative trait loci (QTL) related to agronomic traits being mapped in S. italica, which largely accelerate the molecular breeding process of millet [18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33].…”

Section: Introductionmentioning

confidence: 99%

Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica

Xie

Hou

et al. 2021

BMC Genomics

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Background Foxtail millet (Setaria italica) is one of the oldest domesticated crops and has been considered as an ideal model plant for C4 grasses. It has abundant type of anther and hull colors which is not only a most intuitive morphological marker for color selection in seed production, but also has very important biological significance for the study of molecular mechanism of regulating the synthesis and metabolism of flavonoids and lignin. However, only a few genetic studies have been reported for anther color and hull color in foxtail millet. Results Quantitative trait loci (QTL) analysis for anther color and hull color was conducted using 400 F6 and F7 recombinant inbreed lines (RILs) derived from a cross between parents Yugu18 and Jigu19. Using restriction-site associated DNA sequencing, 43,001 single-nucleotide polymorphisms (SNPs) and 3,022 indels were identified between both the parents and the RILs. A total of 1,304 bin markers developed from the SNPs and indels were used to construct a genetic map that spanned 2196 cM of the foxtail millet genome with an average of 1.68 cM/bin. Combined with this genetic map and the phenotypic data observed in two locations for two years, two QTL located on chromosome 6 (Chr6) in a 1.215-Mb interval (33,627,819–34,877,940 bp) for anther color (yellow - white) and three QTL located on Chr1 in a 6.23-Mb interval (1–6,229,734 bp) for hull color (gold-reddish brown) were detected. To narrow the QTL regions identified from the genetic map and QTL analysis, we developed a new method named “inconsistent rate analysis” and efficiently narrowed the QTL regions of anther color into a 60-kb interval (34.13–34.19 Mb) in Chr6, and narrowed the QTL regions of hull color into 70-kb (5.43–5.50 Mb) and 30-kb (5.69–5.72 Mb) intervals in Chr1. Two genes (Seita.6G228600.v2.2 and Seita.6G228700.v2.2) and a cinnamyl alcohol dehydrogenase (CAD) gene (Seita.1G057300.v2.2) with amino acid changes between the parents detected by whole-genome resequencing were identified as candidate genes for anther and hull color, respectively. Conclusions This work presents the related QTL and candidate genes of anther and hull color in foxtail millet and developed a new method named inconsistent rate analysis to detect the chromosome fragments linked with the quality trait in RILs. This is the first study of the QTL related to hull color in foxtail millet and clarifying that the CAD gene (Seita.1G057300.v2.2) is the key gene responsible for this trait. It lays the foundation for further cloning of the functional genes and provides a powerful tool to detect the chromosome fragments linked with quality traits in RILs.

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“…In addition, increasing sequencing depth rather than marker density (beyond 0.2 per cM) seems to enable greater gains in power of QTL detection in NGS-based BSA studies [ 46 ]. Thus, an efficient strategy could consist in exploiting deep sequencing of genetic libraries representing a reduced part of the genome [ 18 , 46 – 48 ] or targeting the transcriptome [ 28 , 44 , 49 , 50 ] of contrasted bulks. In the counterbalance between bulk size and coverage, favouring larger bulk sizes to the detriment of the depth of sequencing may lead to greater power of detection of QTLs [ 51 ].…”

Section: Discussionmentioning

confidence: 99%

Evaluation of nine statistics to identify QTLs in bulk segregant analysis using next generation sequencing approaches

Cantó

Vigouroux

2022

BMC Genomics

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Background Bulk segregant analysis (BSA) combined with next generation sequencing is a powerful tool to identify quantitative trait loci (QTL). The impact of the size of the study population and the percentage of extreme genotypes analysed have already been assessed. But a good comparison of statistical approaches designed to identify QTL regions using next generation sequencing (NGS) technologies for BSA is still lacking. Results We developed an R code to simulate QTLs in bulks of F2 contrasted lines. We simulated a range of recombination rates based on estimations using different crop species. The simulations were used to benchmark the ability of statistical methods identify the exact location of true QTLs. A single QTL led to a shift in allele frequency across a large fraction of the chromosome for plant species with low recombination rate. The smoothed version of all statistics performed best notably the smoothed Euclidean distance-based statistics was always found to be more accurate in identifying the location of QTLs. We propose a simulation approach to build confidence interval statistics for the detection of QTLs. Conclusion We highlight the statistical methods best suited for BSA studies using NGS technologies in crops even when recombination rate is low. We also provide simulation codes to build confidence intervals and to assess the impact of recombination for application to other studies. This computational study will help select NGS-based BSA statistics that are useful to the broad scientific community.

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Identification of QTL for resistance to leaf blast in foxtail millet by genome re-sequencing analysis

Cited by 17 publications

References 23 publications

Hybridization and introgression in sympatric and allopatric populations of four oak species

Hybridization and introgression in sympatric and allopatric populations of four oak species

Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica

Evaluation of nine statistics to identify QTLs in bulk segregant analysis using next generation sequencing approaches

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