Fine mapping of a Phytophthora-resistance locus RpsGZ in soybean using genotyping-by-sequencing

Abstract Background: Phytophthora root rot (PRR) caused by Phytophthora sojae ( P. sojae ), is one of the most serious limitation to soybean-production in the world. Identification of resistant gene(s) and incorporating them into elite varieties are an effective way for breeding to prevent soybean from being harmed by this disease. A valuable mapping population of 228 F 8:11 recombinant inbred lines (RILs) derived from a cross of resistant cultivar Guizao1 and susceptible cultivar BRSMG68 and a high-density genetic linkage map with an average distance of 0.81 centimorgan (cM) between adjacent bin markers in this population were used to map and explore the candidate gene(s).Results: In this study, the PRR resistance in Guizao1 was controlled by a single Mendelian locus, and was fine mapped to a 367.371-kb genomic region on chromosome 3 that harbours 19 genes, including 7 disease resistance (R)-like genes in the reference Willliams 82 genome. Quantitative real-time PCR assays of possible candidate genes revealed that Glyma.03g05300 was likely involved in PRR resistance.Conclusions: These findings of fine mapping of a novel Rps locus will serve as a basis for cloning, transferring of resistant genes and breeding of P. sojae resistant soybean cultivars through marker-assisted selection.

Download Full-text

Fine mapping of a Phytophthora-resistance locus RpsGZ in soybean using Genotyping-by-Sequencing

10.21203/rs.2.12050/v1 ◽

2019 ◽

Author(s):

Bingzhi Jiang ◽

Yanbo Cheng ◽

Zhandong Cai ◽

Mu Li ◽

Ze Jiang ◽

...

Keyword(s):

Cell Death ◽

Candidate Genes ◽

Fine Mapping ◽

Average Distance ◽

Recombinant Inbred Lines ◽

Enrichment Analysis ◽

Genotyping By Sequencing ◽

Phytophthora Sojae ◽

Resistance Locus ◽

Phytophthora Root Rot

Abstract Background Phytophthora root rot (PRR), caused by Phytophthora sojae is one of the most important soil-borne diseases in many soybean-production regions in the world. Identification of resistant gene(s) and incorporating them into elite varieties are an effective way for breeding to prevent soybean from being harmed by this disease. A valuable mapping population of 228 F8:11 recombinant inbred lines (RILs) derived from a cross of resistant cultivar Guizao1 and susceptible cultivar BRSMG68 and a high-density genetic linkage map with an average distance of 0.81 centimorgan (cM) between adjacent bin markers in this population were used to map and explore the candidate genes. Results In this study, the PRR resistance in Guizao1 was controlled by a single Mendelian locus, and was fine mapped to a 460.702-kb genomic region on chromosome 3 that harbours 20 genes, including 8 disease resistance (R)-like genes in the reference Willliams 82 genome. These 8 candidate genes potentially involved in programmed cell death, cell death, apoptosis and ADP binding by adopting Gene Ontology (GO) enrichment analysis. Conclusions These findings of fine mapping of a novel Rps locus will serve as a basis for cloning, transferring of resistant genes and breeding of P. sojae resistant soybean cultivars through marker-assisted selection.

Download Full-text

High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach

BMC Genomics ◽

10.1186/s12864-021-07788-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Gehendra Bhattarai ◽

Wei Yang ◽

Ainong Shi ◽

Chunda Feng ◽

Braham Dhillon ◽

...

Keyword(s):

Candidate Genes ◽

Downy Mildew ◽

Association Analysis ◽

Spinacia Oleracea ◽

Genotyping By Sequencing ◽

Significant Snps ◽

Snp Markers ◽

Resistance Locus ◽

Downy Mildew Resistance ◽

Mildew Resistance

Abstract Background Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant host and comprises 19 reported races and many novel isolates. Sixteen new P. effusa races were identified during the past three decades, and the new pathogen races are continually overcoming the genetic resistances used in commercial cultivars. A spinach breeding population derived from the cross between cultivars Whale and Lazio was inoculated with P. effusa race 16 in an environment-controlled facility; disease response was recorded and genotyped using genotyping by sequencing (GBS). The main objective of this study was to identify resistance-associated single nucleotide polymorphism (SNP) markers from the cultivar Whale against the P. effusa race 16. Results Association analysis conducted using GBS markers identified six significant SNPs (S3_658,306, S3_692697, S3_1050601, S3_1227787, S3_1227802, S3_1231197). The downy mildew resistance locus from cultivar Whale was mapped to a 0.57 Mb region on chromosome 3, including four disease resistance candidate genes (Spo12736, Spo12784, Spo12908, and Spo12821) within 2.69–11.28 Kb of the peak SNP. Conclusions Genomewide association analysis approach was used to map the P. effusa race 16 resistance loci and identify associated SNP markers and the candidate genes. The results from this study could be valuable in understanding the genetic basis of downy mildew resistance, and the SNP marker will be useful in spinach breeding to select resistant lines.

Download Full-text

Fine mapping of the Rrs1 resistance locus against scald in two large populations derived from Spanish barley landraces

Theoretical and Applied Genetics ◽

10.1007/s00122-013-2196-4 ◽

2013 ◽

Vol 126 (12) ◽

pp. 3091-3102 ◽

Cited By ~ 22

Author(s):

Kerstin Hofmann ◽

Cristina Silvar ◽

Ana M. Casas ◽

Markus Herz ◽

Bianca Büttner ◽

...

Keyword(s):

Fine Mapping ◽

Resistance Locus ◽

Large Populations ◽

Barley Landraces

Download Full-text

Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed Senescence

Genes ◽

10.3390/genes11091026 ◽

2020 ◽

Vol 11 (9) ◽

pp. 1026 ◽

Cited By ~ 1

Author(s):

K. N. S. Usha Kiranmayee ◽

C. Tom Hash ◽

S. Sivasubramani ◽

P. Ramu ◽

Bhanu Prakash Amindala ◽

...

Keyword(s):

Drought Tolerance ◽

Fine Mapping ◽

Mapping Population ◽

Single Gene ◽

Genotyping By Sequencing ◽

Introgression Line ◽

Genomic Region ◽

Stay Green ◽

Delayed Senescence ◽

Genomic Regions

This study was conducted to dissect the genetic basis and to explore the candidate genes underlying one of the important genomic regions on an SBI-10 long arm (L), governing the complex stay-green trait contributing to post-flowering drought-tolerance in sorghum. A fine-mapping population was developed from an introgression line cross—RSG04008-6 (stay-green) × J2614-11 (moderately senescent). The fine-mapping population with 1894 F2 was genotyped with eight SSRs and a set of 152 recombinants was identified, advanced to the F4 generation, field evaluated with three replications over 2 seasons, and genotyped with the GBS approach. A high-resolution linkage map was developed for SBI-10L using 260 genotyping by sequencing—Single Nucleotide Polymorphism (GBS–SNPs). Using the best linear unpredicted means (BLUPs) of the percent green leaf area (%GL) traits and the GBS-based SNPs, we identified seven quantitative trait loci (QTL) clusters and single gene, mostly involved in drought-tolerance, for each QTL cluster, viz., AP2/ERF transcription factor family (Sobic.010G202700), NBS-LRR protein (Sobic.010G205600), ankyrin-repeat protein (Sobic.010G205800), senescence-associated protein (Sobic.010G270300), WD40 (Sobic.010G205900), CPK1 adapter protein (Sobic.010G264400), LEA2 protein (Sobic.010G259200) and an expressed protein (Sobic.010G201100). The target genomic region was thus delimited from 15 Mb to 8 genes co-localized with QTL clusters, and validated using quantitative real-time (qRT)–PCR.

Download Full-text

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

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401091 ◽

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.

Download Full-text

The soybean-Phytophthora resistance locus Rps1-k encompasses coiled coil-nucleotide binding-leucine rich repeat-like genes and repetitive sequences

BMC Plant Biology ◽

10.1186/1471-2229-8-29 ◽

2008 ◽

Vol 8 (1) ◽

pp. 29 ◽

Cited By ~ 53

Author(s):

Hongyu Gao ◽

Madan K Bhattacharyya

Keyword(s):

Repetitive Sequences ◽

Coiled Coil ◽

Nucleotide Binding ◽

Resistance Locus ◽

Leucine Rich Repeat ◽

Phytophthora Resistance

Download Full-text

Confirmation and fine mapping of the resistance locus Ren9 from the grapevine cultivar ‘Regent’

10.1101/2020.11.27.400770 ◽

2020 ◽

Author(s):

Daniel Zendler ◽

Reinhard Töpfer ◽

Eva Zyprian

Keyword(s):

Fine Mapping ◽

Fungal Pathogens ◽

Genetic Resource ◽

Mapping Population ◽

Resistance Breeding ◽

Plasmopara Viticola ◽

Cabernet Sauvignon ◽

Chromosome 15 ◽

Resistance Locus ◽

Grapevine Cultivar

AbstractGrapevine (Vitis vinifera ssp. vinifera) is a major fruit crop with high economic importance. Due to its susceptibility towards fungal pathogens such as Erysiphe necator and Plasmopara viticola, the causal agents of powdery and downy mildew (PM, DM), grapevine growers annually face a major challenge in coping with shortfall of yield caused by these diseases. Here we report the confirmation of a genetic resource for grapevine resistance breeding against PM. During the delimitation process of Ren3 on chromosome 15 from the cultivar ‘Regent’, a second resistance-encoding region on chromosome 15 termed Ren9 was characterized. It mediates a trailing necrosis associated with the appressoria of E. necator and restricts pathogen growth. In this study, we confirm this QTL in a related mapping population of ‘Regent’ x ‘Cabernet Sauvignon’. The data show that this locus is located at the upper arm of chromosome 15 between markers GF15-58 (0.15 Mb) and GF15-53 (4 Mb). The efficiency of the resistance against one of the prominent European PM isolates (EU-B) is demonstrated. Based on fine-mapping and literature knowledge we propose two possible regions of interest and supply genetic markers to follow both regions in marker assisted selection.

Download Full-text