scholarly journals Map and sequence-based chromosome walking towards cloning of the male fertility restoration gene Rf5 linked to R11 in sunflower

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Guojia Ma ◽  
Yunming Long ◽  
Qijian Song ◽  
Zahirul I. Talukder ◽  
Md Shamimuzzaman ◽  
...  
Keyword(s):  
Fine Mapping ◽  
Fertility Restoration ◽  
Snp Markers ◽  
Pentatricopeptide Repeat ◽  
Fertility Restorer ◽  
Target Region ◽  
Donor Line ◽  
Density Map ◽  
Encoding Gene ◽  
Whole Genome Resequencing

AbstractThe nuclear fertility restorer gene Rf5 in HA-R9, originating from the wild sunflower species Helianthus annuus, is able to restore the widely used PET1 cytoplasmic male sterility in sunflowers. Previous mapping placed Rf5 at an interval of 5.8 cM on sunflower chromosome 13, distal to a rust resistance gene R11 at a 1.6 cM genetic distance in an SSR map. In the present study, publicly available SNP markers were further mapped around Rf5 and R11 using 192 F2 individuals, reducing the Rf5 interval from 5.8 to 0.8 cM. Additional SNP markers were developed in the target region of the two genes from the whole-genome resequencing of HA-R9, a donor line carrying Rf5 and R11. Fine mapping using 3517 F3 individuals placed Rf5 at a 0.00071 cM interval and the gene co-segregated with SNP marker S13_216392091. Similarly, fine mapping performed using 8795 F3 individuals mapped R11 at an interval of 0.00210 cM, co-segregating with two SNP markers, S13_225290789 and C13_181790141. Sequence analysis identified Rf5 as a pentatricopeptide repeat-encoding gene. The high-density map and diagnostic SNP markers developed in this study will accelerate the use of Rf5 and R11 in sunflower breeding.

scholarly journals Association Mapping of Fertility Restorer Gene for CMS PET1 in Sunflower

Agronomy ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 49 ◽  
Author(s):  
Denis Goryunov ◽  
Irina Anisimova ◽  
Vera Gavrilova ◽  
Alina Chernova ◽  
Evgeniia Sotnikova ◽  
...  
Keyword(s):  
Association Mapping ◽  
Molecular Mechanisms ◽  
Genome Wide Association Study ◽  
Fertility Restoration ◽  
Restorer Gene ◽  
Pentatricopeptide Repeat ◽  
Time Data ◽  
Fertility Restorer ◽  
Practical Utilization ◽  
Fertility Restorer Gene

The phenomenon of cytoplasmic male sterility (CMS), consisting in the inability to produce functional pollen due to mutations in mitochondrial genome, has been described in more than 150 plant species. With the discovery of nuclear fertility restorer (Rf) genes capable of suppressing the CMS phenotype, it became possible to use the CMS-Rf genetic systems as the basis for practical utilization of heterosis effect in various crops. Seed production of sunflower hybrids all over the world is based on the extensive use of the PET1 CMS combined with the Rf1 gene. At the same time, data on Rf1 localization, sequence, and molecular basis for the CMS PET1 type restoration of fertility remain unknown. Searching for candidate genes of the Rf1 gene has great fundamental and practical value. Therefore, in this study, association mapping of fertility restorer gene for CMS PET1 in sunflower was performed. The genome-wide association study (GWAS) results made it possible to isolate a segment 7.72 Mb in length on chromosome 13, in which 21 candidates for Rf1 fertility restorer gene were identified, including 20 pentatricopeptide repeat (PPR)family genes and one Probable aldehyde dehydrogenase gene. The results will serve as a basis for further study of the genetic nature and molecular mechanisms of pollen fertility restoration in sunflower, as well as for further intensification of sunflower breeding.

QTL Identification, Fine Mapping, and Marker Development for Breeding Peanut (Arachis hypogaea L.) Resistant to Bacterial Wilt

2021 ◽  
Author(s):  
Feiyan Qi ◽  
Ziqi Sun ◽  
Hua Liu ◽  
Zheng Zheng ◽  
Li Qin ◽  
...  
Keyword(s):  
Fine Mapping ◽  
Bacterial Wilt ◽  
Snp Markers ◽  
Potential Contribution ◽  
Marker Assisted Breeding ◽  
Wilt Resistance ◽  
Bacterial Wilt Resistance ◽  
Disease Resistant ◽  
Resistant Varieties ◽  
Whole Genome Resequencing

Abstract Bacterial wilt, caused by Ralstonia solanacearum, is a major disease detrimental to peanut production in China. Breeding disease-resistant peanut varieties is the most economical and effective way to prevent the disease and yield loss. Fine mapping the QTLs for bacterial wilt resistance is critical for the marker-assisted breeding of disease-resistant varieties. A recombinant inbred population comprising 512 lines was used to construct a high-density genetic linkage map and to identify QTLs for bacterial wilt resistance following restriction-site-associated DNA sequencing. The genetic map, which included 5,120 SNP markers, covered a length of 3,184 cM with an average marker distance of 0.6 cM. Four QTLs for bacterial wilt resistance were mapped on four chromosomes. One major QTL, qBWA12, was stably detected in all four development stages investigated over the three trail years. Additionally, qBWA12 spanned a 2.6 cM region, corresponding to approximately 0.4 Mb and was fine mapped to a 216.7 kb region by applying KASP markers that were polymorphic between the two parents based on whole-genome resequencing data. In a large collection of breeding and germplasm lines, it was proved that KASP marker A12.4097252 can be applied for the marker-assisted breeding to develop peanut varieties resistant to bacterial wilt. Of the 19 candidate genes in the region covered by qBWA12, nine NBS-LRR genes should be further investigated regarding their potential contribution to the resistance of peanut against bacterial wilt.

scholarly journals Identification of Rf9, a Gene Contributing to the Genetic Complexity of Fertility Restoration in Hybrid Wheat

2020 ◽  
Vol 11 ◽  
Author(s):  
Fahimeh Shahinnia ◽  
Manuel Geyer ◽  
Annette Block ◽  
Volker Mohler ◽  
Lorenz Hartl
Keyword(s):  
Fertility Restoration ◽  
Snp Markers ◽  
Genetic Maps ◽  
Hybrid Seed Production ◽  
Hybrid Wheat ◽  
Pentatricopeptide Repeat ◽  
Male Sterile ◽  
Transcription Termination Factor ◽  
Restorer Of Fertility ◽  
Genes Encoding

Wheat (Triticum aestivum L.) is a self-pollinating crop whose hybrids offer the potential to provide a major boost in yield. Male sterility induced by the cytoplasm of Triticum timopheevii is a powerful method for hybrid seed production. Hybrids produced by this method are often partially sterile, and full fertility restoration is crucial for wheat production using hybrid cultivars. To identify the genetic loci controlling fertility restoration in wheat, we produced two cytoplasmic male-sterile (CMS) backcross (BC1) mapping populations. The restorer lines Gerek 79 and 71R1203 were used to pollinate the male-sterile winter wheat line CMS-Sperber. Seed set and numbers of sterile spikelets per spike were evaluated in 340 and 206 individuals of the populations derived from Gerek 79 and 71R1203, respectively. Genetic maps were constructed using 930 and 994 single nucleotide polymorphism (SNP) markers, spanning 2,160 and 2,328 cM over 21 linkage groups in the two populations, respectively. Twelve quantitative trait loci (QTL) controlled fertility restoration in both BC1 populations, including a novel restorer-of-fertility (Rf) locus flanked by the SNP markers IWB72413 and IWB1550 on chromosome 6AS. The locus was mapped as a qualitative trait in the BC1 Gerek 79 population and was designated Rf9. One hundred-nineteen putative candidate genes were predicted within the QTL region on chromosome 6AS. Among them were genes encoding mitochondrial transcription termination factor and pentatricopeptide repeat-containing proteins that are known to be associated with fertility restoration. This finding is a promising step to better understand the functions of genes for improving fertility restoration in hybrid wheat.

scholarly journals Identification of a new gene Rf9 and unravelling the genetic complexity for controlling fertility restoration in hybrid wheat

2020 ◽  
Author(s):  
Fahimeh Shahinnia ◽  
Manuel Geyer ◽  
Annette Block ◽  
Volker Mohler ◽  
Lorenz Hartl
Keyword(s):  
Fertility Restoration ◽  
Triticum Aestivum L ◽  
Snp Markers ◽  
Genetic Maps ◽  
Hybrid Seed Production ◽  
Hybrid Wheat ◽  
Pentatricopeptide Repeat ◽  
Male Sterile ◽  
Genes Encoding ◽  
New Gene

AbstractWheat (Triticum aestivum L.) is a self-pollinating crop whose hybrids offer the potential to provide a major boost in yield. Male sterility induced by the cytoplasm of Triticum timopheevii is a powerful method for hybrid seed production. Hybrids produced by this method are often partially sterile and full fertility restoration is crucial for wheat production using hybrid cultivars. To identify genetic loci controlling fertility restoration in wheat, we produced two CMS-based backcross (BC1) mapping populations. The restorer lines Gerek 79 and 71R1203 were used to pollinate the male-sterile winter wheat line CMS-Sperber. Seed set and numbers of sterile spikelets per spike were evaluated in 340 and 206 individuals of the populations derived from Gerek 79 and 71R1203, respectively. Genetic maps were constructed using 930 and 994 SNPs, spanning 2,160 and 2,328 cM over 21 linkage groups in the two populations, respectively. Twelve quantitative trait loci (QTL) controlled fertility restoration in both BC1 populations, including a novel restorer-of-fertility (Rf) locus flanked by the single nucleotide polymorphism (SNP) markers IWB72413 and IWB1550 on chromosome 6AS. The locus was mapped as a qualitative trait in the BC1 Gerek 79 population and was designated Rf9. Ninety-three putative candidate genes were predicted for the QTL region on chromosome 6AS. Among them were genes encoding tetratricopeptide and pentatricopeptide repeat-containing proteins in rice known to be associated with fertility restoration. This finding is a promising step to better understand the functions of genes for improving hybrid wheat.

scholarly journals Mutator-Induced Mutations of the rf1 Nuclear Fertility Restorer of T-Cytoplasm Maize Alter the Accumulation of T-urfl3 Mitochondrial Transcripts

Genetics ◽  
1996 ◽  
Vol 143 (3) ◽  
pp. 1383-1394
Author(s):  
Roger P Wise ◽  
Carren L Dill ◽  
Patrick S Schnable
Keyword(s):  
Pollen Fertility ◽  
Fertility Restoration ◽  
Mitochondrial Rna ◽  
Induced Mutations ◽  
Male Sterile ◽  
Fertility Restorer ◽  
Restorer Genes ◽  
Mitochondrial Transcripts ◽  
Ecori Restriction ◽  
Fertility Restorer Genes

Abstract Dominant alleles of the rf1 and rf2 nuclear-encoded fertility restorer genes are necessary for restoration of pollen fertility in T-cytoplasm maize. To further characterize fertility restoration mediated by the Rf1 allele, 123,500 gametes derived from plants carrying the Mutator transposable element family were screened for rf1-mutant alleles (rf1-m) Four heritable rf1-m alleles were recovered from these populations. Three rf1-m alleles were derived from the progenitor allele Rf1-IAl53 and one was derived from Rf1-Ky21. Cosegregation analysis revealed 5.5- and 2.4kb Mu1-hybridizing EcoRI restriction fragments in all of the male-sterile and none of the male-fertile plants in families segregating for rf1-m3207 and rf1-m3310, respectively. Mitochondrial RNA gel blot analyses indicated that all four rf1-m alleles in male-sterile plants cosegregated with the altered steady-state accumulation of 1.6 and O.6-kb T-urf13 transcripts, demonstrating that these transcripts are Rf1 dependent. Plants carrying a leaky mutant, rf1-m7323, revealed variable levels of Rf1-associated, T-urf13 transcripts and the degree of pollen fertility. The ability to obtain rf1-m derivatives from Rf1 indicates that Rf1 alleles produce a functional gene product necessary for the accumulation of specific T-urf13 transcripts in T-cytoplasm maize.

scholarly journals A single nucleotide substitution in the coding region of Ogura male sterile gene, orf138, determines effectiveness of a fertility restorer gene, Rfo, in radish

2021 ◽  
Author(s):  
Hiroshi Yamagishi ◽  
Megumi Jikuya ◽  
Kanako Okushiro ◽  
Ayako Hashimoto ◽  
Asumi Fukunaga ◽  
...  
Keyword(s):  
Male Sterility ◽  
Nucleotide Substitution ◽  
Fertility Restoration ◽  
Type A ◽  
Restorer Gene ◽  
Single Nucleotide Substitution ◽  
Coding Region ◽  
Fertility Restorer ◽  
Single Nucleotide ◽  
Fertility Restorer Gene

AbstractCytoplasmic male sterility (CMS) observed in many plants leads defect in the production of functional pollen, while the expression of CMS is suppressed by a fertility restorer gene in the nuclear genome. Ogura CMS of radish is induced by a mitochondrial orf138, and a fertility restorer gene, Rfo, encodes a P-type PPR protein, ORF687, acting at the translational level. But, the exact function of ORF687 is still unclear. We found a Japanese variety showing male sterility even in the presence of Rfo. We examined the pollen fertility, Rfo expression, and orf138 mRNA in progenies of this variety. The progeny with Type H orf138 and Rfo showed male sterility when their orf138 mRNA was unprocessed within the coding region. By contrast, all progeny with Type A orf138 were fertile though orf138 mRNA remained unprocessed in the coding region, demonstrating that ORF687 functions on Type A but not on Type H. In silico analysis suggested a specific binding site of ORF687 in the coding region, not the 5′ untranslated region estimated previously, of Type A. A single nucleotide substitution in the putative binding site diminishes affinity of ORF687 in Type H and is most likely the cause of the ineffectiveness of ORF687. Furthermore, fertility restoration by RNA processing at a novel site in some progeny plants indicated a new and the third fertility restorer gene, Rfs, for orf138. This study clarified that direct ORF687 binding to the coding region of orf138 is essential for fertility restoration by Rfo.

scholarly journals Comprehensive Transcriptome Analyses Reveal Candidate Genes for Variation in Seed Size/Weight During Peanut (Arachis hypogaea L.) Domestication

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhongfeng Li ◽  
Xingguo Zhang ◽  
Kunkun Zhao ◽  
Kai Zhao ◽  
Chengxin Qu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Seed Development ◽  
Seed Size ◽  
Snp Markers ◽  
Pentatricopeptide Repeat ◽  
Significant Differential Expression ◽  
Ppr Protein ◽  
Cultivated Peanut ◽  
Transcriptome Analyses ◽  
Wild Peanut

Seed size/weight, a key domestication trait, is also an important selection target during peanut breeding. However, the mechanisms that regulate peanut seed development are unknown. We re-sequenced 12 RNA samples from developing seeds of two cultivated peanut accessions (Lines 8106 and 8107) and wild Arachis monticola at 15, 30, 45, and 60 days past flowering (DPF). Transcriptome analyses showed that ∼36,000 gene loci were expressed in each of the 12 RNA samples, with nearly half exhibiting moderate (2 ≤ FPKM < 10) expression levels. Of these genes, 12.2% (4,523) were specifically expressed during seed development, mainly at 15 DPF. Also, ∼12,000 genes showed significant differential expression at 30, 45, and/or 60 DPF within each of the three peanut accessions, accounting for 31.8–34.1% of the total expressed genes. Using a method that combined comprehensive transcriptome analysis and previously mapped QTLs, we identified several candidate genes that encode transcription factor TGA7, topless-related protein 2, IAA-amino acid hydrolase ILR1-like 5, and putative pentatricopeptide repeat-containing (PPR) protein. Based on sequence variations identified in these genes, SNP markers were developed and used to genotype both 30 peanut landraces and a genetic segregated population, implying that EVM0025654 encoding a PPR protein may be associated with the increased seed size/weight of the cultivated accessions in comparison with the allotetraploid wild peanut. Our results provide additional knowledge for the identification and functional research into candidate genes responsible for the seed size/weight phenotype in peanut.

scholarly journals Genetic Analysis and Fine Mapping of a Spontaneously Mutated Male Sterility Gene in Brassica rapa ssp. chinensis

2020 ◽  
Vol 10 (4) ◽  
pp. 1309-1318
Author(s):  
Tzu-Kai Lin ◽  
Ya-Ping Lin ◽  
Shun-Fu Lin
Keyword(s):  
Male Sterility ◽  
Fine Mapping ◽  
Genotyping By Sequencing ◽  
Snp Markers ◽  
Hybrid Seed Production ◽  
Spontaneous Mutant ◽  
Male Sterile ◽  
Sterility Gene ◽  
Intron 4 ◽  
Male Sterility Gene

Male sterility has been widely used in hybrid seed production in Brassica, but not in B. rapa ssp. chinensis, and genetic models of male sterility for this subspecies are unclear. We discovered a spontaneous mutant in B. rapa ssp. chinensis. A series of progeny tests indicated that male sterility in B. rapa ssp. chinensis follows a three-allele model with BrMsa, BrMsb, and BrMsc. The male sterility locus has been mapped to chromosome A07 in BC1 and F2 populations through genotyping by sequencing. Fine mapping in a total of 1,590 F2 plants narrowed the male sterility gene BrMs to a 400 kb region, with two SNP markers only 0.3 cM from the gene. Comparative gene mapping shows that the Ms gene in B. rapa ssp. pekinensis is different from the BrMs gene of B. rapa ssp. chinensis, despite that both genes are located on chromosome A07. Interestingly, the DNA sequence orthologous to a male sterile gene in Brassica napus, BnRf, is within 400 kb of the BrMs locus. The BnRf orthologs of B. rapa ssp. chinensis were sequenced, and one KASP marker (BrMs_indel) was developed for genotyping based on a 14 bp indel at intron 4. Cosegregation of male sterility and BrMs_indel genotypes in the F2 population indicated that BnRf from B. napus and BrMs from B. rapa are likely to be orthologs. The BrMs_indel marker developed in this study will be useful in marker-assisted selection for the male sterility trait.

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