scholarly journals Physical mapping and InDel marker development for the restorer gene Rf2 in cytoplasmic male sterile CMS-D8 cotton

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Juanjuan Feng ◽  
Xuexian Zhang ◽  
Meng Zhang ◽  
Liping Guo ◽  
Tingxiang Qi ◽  
...  
Keyword(s):  
High Throughput ◽  
Physical Mapping ◽  
Snp Genotyping ◽  
Restorer Line ◽  
Male Sterile ◽  
Cytoplasmic Male Sterile ◽  
Qrt Pcr ◽  
Indel Markers ◽  
Selection Of ◽  
Candidate Interval

Abstract Background Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 containing Rf2 gene can restore the fertility of the corresponding sterile line. This study combined the whole genome resequencing bulked segregant analysis (BSA) with high-throughput SNP genotyping to accelerate the physical mapping of Rf2 locus in CMS-D8 cotton. Methods The fertility of backcross population ((sterile line×restorer line)×maintainer line) comprising of 1623 individuals was investigated in the field. The fertile pool (100 plants with fertile phenotypes, F-pool) and the sterile pool (100 plants with sterile phenotypes, S-pool) were constructed for BSA resequencing. The selection of 24 single nucleotide polymorphisms (SNP) through high-throughput genotyping and the development insertion and deletion (InDel) markers were conducted to narrow down the candidate interval. The pentapeptide repeat (PPR) family genes and upregulated genes in restore line in the candidate interval were analysed by qRT-PCR. Results The fertility investigation results showed that fertile and sterile separation ratio was consistent with 1:1. BSA resequencing technology, high-throughput SNP genotyping, and InDel markers were used to identify Rf2 locus on candidate interval of 1.48 Mb on chromosome D05. Furthermore, it was quantified in this experiment that InDel markers co-segregated with Rf2 enhanced the selection of the restorer line. The qRT-PCR analysis revealed PPR family gene Gh_D05G3391 located in candidate interval had significantly lower expression than sterile and maintainer lines. In addition, utilization of anther RNA-Seq data of CMS-D8 identified that the expression level of Gh_D05G3374 encoding NB-ARC domain-containing disease resistance protein in restorer lines was significantly higher than that in sterile and maintainer lines. Conclusions This study not only enabled us to precisely locate the restore gene Rf2 but also evaluated the utilization of InDel markers for marker assisted selection in the CMS-D8 Rf2 cotton breeding line. The results of this study provide an important foundation for further studies on the mapping and cloning of restorer genes.

scholarly journals Physical mapping and InDel marker development for the restorer gene Rf2 in cytoplasmic male sterile CMS-D8 cotton 

2021 ◽  
Author(s):  
Juanjuan Feng ◽  
Xuexian Zhang ◽  
Meng Zhang ◽  
Liping Guo ◽  
Tingxiang QI ◽  
...  
Keyword(s):  
High Throughput ◽  
Physical Mapping ◽  
Snp Genotyping ◽  
Restorer Line ◽  
Male Sterile ◽  
Cytoplasmic Male Sterile ◽  
Qrt Pcr ◽  
Indel Markers ◽  
Selection Of ◽  
Candidate Interval

Abstract Background: Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 containing Rf2 gene can restore the fertility of the corresponding sterile line. This study combined the whole genome resequencing bulked segregant analysis (BSA) with high-throughput SNP genotyping to accelerate the physical mapping of Rf2 locus in CMS-D8 cotton. Methods: The fertility of backcross population ((sterile line×restorer line)×maintainer line) comprising of 1623 individuals was investigated in the field. The fertile pool (100 plants with fertile phenotypes, F-pool) and the sterile pool (100 plants with sterile phenotypes, S-pool) were constructed for BSA resequencing. The selection of 24 single nucleotide polymorphisms (SNP) through high-throughput genotyping and the development insertion and deletion (InDel) markers were conducted to narrow down the candidate interval. The pentapeptide repeat (PPR) family genes and upregulated genes in restore line in the candidate interval were analysed by qRT-PCR. Results: The fertility investigation results showed that fertile and sterile separation ratio was consistent with 1:1. BSA resequencing technology, high-throughput SNP genotyping, and InDel markers were used to identify Rf2 locus on candidate interval of 1.48 Mb on Chromosome D05. Furthermore, it was quantified in this experiment that InDel markers co-segregated with Rf2 enhanced the selection of the restorer line. The qRT-PCR analysis revealed PPR family gene Gh_D05G3391 located in candidate interval had significantly lower expression than sterile and maintainer lines. In addition, utilization of anther RNA-Seq data of CMS-D8 identified that the expression level of Gh_D05G3374 encoding NB-ARC domain-containing disease resistance protein in restorer lines was significantly higher than that in sterile and maintainer lines. Conclusions: This study not only enabled us to precisely locate the restore gene Rf2 but also evaluated the utilization of InDel markers for marker assisted selection in the CMS-D8 Rf2 cotton breeding line. The results of this study provide an important foundation for further studies on the mapping and cloning of restorer genes.

scholarly journals Physical mapping and InDel marker development for the restorer gene Rf2 in cytoplasmic male sterile CMS-D8 cotton

2020 ◽  
Author(s):  
Juanjuan Feng ◽  
Xuexian Zhang ◽  
Meng Zhang ◽  
Liping Guo ◽  
Tingxiang QI ◽  
...  
Keyword(s):  
High Throughput ◽  
Physical Mapping ◽  
Snp Genotyping ◽  
Restorer Line ◽  
Male Sterile ◽  
Cytoplasmic Male Sterile ◽  
Qrt Pcr ◽  
Indel Markers ◽  
Selection Of ◽  
Candidate Interval

Abstract Background: Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 containing Rf 2 gene can restore the fertility of the corresponding sterile line. This study combined the whole genome resequencing bulked segregant analysis (BSA) with high-throughput SNP genotyping to accelerate the physical mapping of Rf 2 locus in CMS-D8 cotton. Methods: The fertility of backcross population ((sterile line×restorer line)×maintainer line) comprising of 1623 individuals was investigated in the field. The fertile pool (100 plants with fertile phenotypes, F-pool) and the sterile pool (100 plants with sterile phenotypes, S-pool) were constructed for BSA resequencing. The selection of 24 single nucleotide polymorphisms (SNP) through high-throughput genotyping and the development insertion and deletion (InDel) markers were conducted to narrow down the candidate interval. The pentapeptide repeat (PPR) family genes and upregulated genes in restore line in the candidate interval were analysed by qRT-PCR. Results: The fertility investigation results showed that fertile and sterile separation ratio was consistent with 1:1. BSA resequencing technology, high-throughput SNP genotyping, and InDel markers were used to identify Rf 2 locus on candidate interval of 1.48 Mb on Chromosome D05. Furthermore, it was quantified in this experiment that InDel markers co-segregated with Rf 2 enhanced the selection of the restorer line. The qRT-PCR analysis revealed PPR family gene Gh_D05G3391 located in candidate interval had significantly lower expression than sterile and maintainer lines. In addition, utilization of anther RNA-Seq data of CMS-D8 identified that the expression level of Gh_D05G3374 encoding NB-ARC domain-containing disease resistance protein in restorer lines was significantly higher than that in sterile and maintainer lines. Conclusions: This study not only enabled us to precisely locate the restore gene Rf 2 but also evaluated the utilization of InDel markers for marker assisted selection in the CMS-D8 Rf 2 cotton breeding line. The results of this study provide an important foundation for further studies on the mapping and cloning of restorer genes.

scholarly journals Physical mapping and InDel marker development for the restorer gene Rf2 in cytoplasmic male sterile CMS-D8 cotton

2020 ◽  
Author(s):  
Juanjuan Feng ◽  
Xuexian Zhang ◽  
Meng Zhang ◽  
Liping Guo ◽  
Tingxiang QI ◽  
...  
Keyword(s):  
High Throughput ◽  
Physical Mapping ◽  
Snp Genotyping ◽  
Restorer Line ◽  
Male Sterile ◽  
Backcross Population ◽  
Cytoplasmic Male Sterile ◽  
Indel Markers ◽  
Selection Of ◽  
Candidate Interval

Abstract Background Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 containing Rf2 gene can restore the fertility of the corresponding sterile line. This study combined the whole genome resequencing bulked segregant analysis (BSA) with high-throughput SNP genotyping to accelerate the physical mapping of Rf2 locus in CMS-D8 cotton. Methods The fertility of backcross population ((sterile line × restorer line) × maintainer line) comprising of 1623 individuals was investigated in the field. The fertile pool (100 plants with fertile phenotypes, F-pool) and the sterile pool (100 plants with sterile phenotypes, S-pool) were constructed for BSA resequencing. Selection of 24 SNPs through high-throughput genotyping and development InDel markers narrow down the candidate interval. The PPR genes and restore line up-regulated genes in the candidate interval were analyzed by RT-PCR. Results The fertility investigation results showed that fertile and sterile separation ratio was consistent with 1:1. BSA resequencing technology, high-throughput SNP genotyping, and InDel markers were used to identify Rf2 locus on candidate interval of 1.48 Mb on Chromosome D05. Furthermore, it was quantified in this experiment that InDel markers co-segregated with Rf2 enhanced the selection of the restorer line. The qRT-PCR analysis revealed PPR family gene Gh_D05G3391 located in candidate interval had significantly lower expression than sterile and maintainer lines. In addition, utilization of previous anther RNA-Seq data of CMS-D8 identified that the expression level of Gh_D05G3374 encoding NB-ARC domain-containing disease resistance protein in restorer lines was significantly higher than that in sterile and maintainer lines. Conclusions This study not only enabled us to precise locate the restore gene Rf2 but also evaluated the utilization of InDel markers for marker assisted selection in CMS-D8 Rf2 cotton breeding line. The results of this study provide an important foundation for further studies on the mapping and cloning of restorer genes.

scholarly journals DETERMINATION OF CYTOPLASMIC MALE STERILE FACTORS IN ONION PLANTS ( ALLIUM CEPA L.) OF VNIISSOK'S BREEDING

2011 ◽  
pp. 20-21
Author(s):  
T.P. Suprunova ◽  
A.N. Logunov ◽  
V.V. Logunova ◽  
A.F. Agafonov
Keyword(s):  
Molecular Markers ◽  
High Throughput ◽  
Mitochondrial Genes ◽  
Pcr Markers ◽  
Male Sterile ◽  
Cytoplasmic Male Sterile ◽  
Breeding Populations ◽  
Allium Cepa L ◽  
Allelic Variations

Molecular markers were used for screening of the onion plants of VNIISSOK's breeding for cytoplasmic male sterility. Allelic variations of the mitochondrial genes orfА501 and cob were reveled among studied onion samples. Use of the PCR-markers for these genes allowed identifying the cytoplasmic types of 14 onion genotypes. Application of these molecular markers in breeding program could help to select genotypes wit certain type of cytoplasm and may be useful for high throughput identification of cytoplasmic male sterile factors in large onion breeding populations.

scholarly journals Detecting SARS-CoV-2 variants with SNP genotyping

2020 ◽  
Author(s):  
Helen Harper ◽  
Amanda J. Burridge ◽  
Mark Winfield ◽  
Adam Finn ◽  
Andrew D. Davidson ◽  
...  
Keyword(s):  
High Throughput ◽  
Low Cost ◽  
Cost Effective ◽  
Snp Genotyping ◽  
Clinical Samples ◽  
Marker Panel ◽  
Qrt Pcr ◽  
Crucial Information ◽  
The Uk ◽  
Genotyping Panel

AbstractTracking genetic variations from positive SARS-CoV-2 samples yields crucial information about the number of variants circulating in an outbreak and the possible lines of transmission but sequencing every positive SARS-CoV-2 sample would be prohibitively costly for population-scale test and trace operations. Genotyping is a rapid, high-throughput and low-cost alternative for screening positive SARS-CoV-2 samples in many settings. We have designed a SNP identification pipeline to identify genetic variation using sequenced SARS-CoV-2 samples. Our pipeline identifies a minimal marker panel that can define distinct genotypes. To evaluate the system we developed a genotyping panel to detect variants-identified from SARS-CoV-2 sequences surveyed between March and May 2020- and tested this on 50 stored qRT-PCR positive SARS-CoV-2 clinical samples that had been collected across the South West of the UK in April 2020. The 50 samples split into 15 distinct genotypes and there was a 76% probability that any two randomly chosen samples from our set of 50 would have a distinct genotype. In a high throughput laboratory, qRT-PCR positive samples pooled into 384-well plates could be screened with our marker panel at a cost of < £1.50 per sample. Our results demonstrate the usefulness of a SNP genotyping panel to provide a rapid, cost-effective, and reliable way to monitor SARS-CoV-2 variants circulating in an outbreak. Our analysis pipeline is publicly available and will allow for marker panels to be updated periodically as viral genotypes arise or disappear from circulation.

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