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

2020 ◽  
Author(s):  
Bingzhi Jiang ◽  
Yanbo Cheng ◽  
Zhandong Cai ◽  
Mu Li ◽  
Ze Jiang ◽  
...  
Keyword(s):  
Fine Mapping ◽  
Genetic Linkage Map ◽  
Average Distance ◽  
Recombinant Inbred Lines ◽  
Genotyping By Sequencing ◽  
Genomic Region ◽  
Phytophthora Sojae ◽  
Resistance Locus ◽  
Phytophthora Root Rot ◽  
Phytophthora Resistance

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.

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

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.

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

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Bingzhi Jiang ◽  
Yanbo Cheng ◽  
Zhandong Cai ◽  
Mu Li ◽  
Ze Jiang ◽  
...  
Keyword(s):  
Fine Mapping ◽  
Genotyping By Sequencing ◽  
Resistance Locus ◽  
Phytophthora Resistance

scholarly journals Genetic Mapping and Molecular Characterization of a Broad-spectrum Phytophthora sojae Resistance Gene in Chinese Soybean

2019 ◽  
Vol 20 (8) ◽  
pp. 1809 ◽  
Author(s):  
Chao Zhong ◽  
Yinping Li ◽  
Suli Sun ◽  
Canxing Duan ◽  
Zhendong Zhu
Keyword(s):  
Genetic Mapping ◽  
Candidate Gene ◽  
Broad Spectrum ◽  
Genomic Region ◽  
Phytophthora Sojae ◽  
Genetic Population ◽  
Phytophthora Root Rot ◽  
Different Origins ◽  
Lrr Domain

Phytophthora root rot (PRR) causes serious annual soybean yield losses worldwide. The most effective method to prevent PRR involves growing cultivars that possess genes conferring resistance to Phytophthora sojae (Rps). In this study, QTL-sequencing combined with genetic mapping was used to identify RpsX in soybean cultivar Xiu94-11 resistance to all P. sojae isolates tested, exhibiting broad-spectrum PRR resistance. Subsequent analysis revealed RpsX was located in the 242-kb genomic region spanning the RpsQ locus. However, a phylogenetic investigation indicated Xiu94-11 carrying RpsX is distantly related to the cultivars containing RpsQ, implying RpsX and RpsQ have different origins. An examination of candidate genes revealed RpsX and RpsQ share common nonsynonymous SNP and a 144-bp insertion in the Glyma.03g027200 sequence encoding a leucine-rich repeat (LRR) region. Glyma.03g027200 was considered to be the likely candidate gene of RpsQ and RpsX. Sequence analyses confirmed that the 144-bp insertion caused by an unequal exchange resulted in two additional LRR-encoding fragments in the candidate gene. A marker developed based on the 144-bp insertion was used to analyze the genetic population and germplasm, and proved to be useful for identifying the RpsX and RpsQ alleles. This study implies that the number of LRR units in the LRR domain may be important for PRR resistance in soybean.

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

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1026 ◽  
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.

scholarly journals Fine Mapping and Identification of a Novel Phytophthora Root Rot Resistance Locus RpsZS18 on Chromosome 2 in Soybean

2018 ◽  
Vol 9 ◽  
Author(s):  
Chao Zhong ◽  
Suli Sun ◽  
Liangliang Yao ◽  
Junjie Ding ◽  
Canxing Duan ◽  
...  
Keyword(s):  
Fine Mapping ◽  
Root Rot ◽  
Resistance Locus ◽  
Chromosome 2 ◽  
Phytophthora Root Rot

scholarly journals Tightly linked Rps12 and Rps13 genes provide broad-spectrum Phytophthora resistance in soybean

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dipak K. Sahoo ◽  
Anindya Das ◽  
Xiaoqiu Huang ◽  
Silvia Cianzio ◽  
Madan K. Bhattacharyya
Keyword(s):  
Broad Spectrum ◽  
Recombinant Inbred Lines ◽  
Single Gene ◽  
Rapid Evolution ◽  
Phytophthora Sojae ◽  
Oomycete Pathogen ◽  
Break Points ◽  
Phytophthora Resistance ◽  
Or Gene ◽  
Serious Disease

AbstractThe Phytophtora root and stem rot is a serious disease in soybean. It is caused by the oomycete pathogen Phytophthora sojae. Growing Phytophthora resistant cultivars is the major method of controlling this disease. Resistance is race- or gene-specific; a single gene confers immunity against only a subset of the P. sojae isolates. Unfortunately, rapid evolution of new Phytophthora sojae virulent pathotypes limits the effectiveness of an Rps (“resistance to Phytophthora sojae”) gene to 8–15 years. The current study was designed to investigate the effectiveness of Rps12 against a set of P. sojae isolates using recombinant inbred lines (RILs) that contain recombination break points in the Rps12 region. Our study revealed a unique Rps gene linked to the Rps12 locus. We named this novel gene as Rps13 that confers resistance against P. sojae isolate V13, which is virulent to recombinants that contains Rps12 but lack Rps13. The genetic distance between the two Rps genes is 4 cM. Our study revealed that two tightly linked functional Rps genes with distinct race-specificity provide broad-spectrum resistance in soybean. We report here the molecular markers for incorporating the broad-spectrum Phytophthora resistance conferred by the two Rps genes in commercial soybean cultivars.

scholarly journals A Genetic Linkage Map for Watermelon Derived from Recombinant Inbred Lines

2004 ◽  
Vol 129 (2) ◽  
pp. 237-243 ◽  
Author(s):  
Renbing Zhang ◽  
Yong Xu ◽  
Ke Yi ◽  
Haiying Zhang ◽  
Ligong Liu ◽  
...  
Keyword(s):  
Linkage Map ◽  
Recombinant Inbred ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Citrullus Lanatus ◽  
Average Distance ◽  
Recombinant Inbred Lines ◽  
Plant Introduction ◽  
Inter Simple Sequence Repeat ◽  
Inbred Lines

A genetic linkage map was constructed for watermelon using 117 recombinant inbred lines (RILs) (F2S7) descended from a cross between the high quality inbred line 97103 [Citrullus lanatus var. lanatus (Thunb.) Matsum. & Nakai] and the Fusarium wilt (races 0, 1, and 2) resistant U.S. Plant Introduction (PI) 296341 (C. lanatus var. citroides). The linkage map contains 87 randomly amplified polymorphic DNA (RAPD) markers, 13 inter simple sequence repeat (ISSR) markers, and four sequenced characterized amplified region (SCAR) markers. The map consists of 15 linkage groups. Among them are a large linkage group of 31 markers covering a mapping distance of 277.5 cM, six groups each with 4 to 12 markers covering a mapping distance of 51.7 to 172.2 cM, and eight small groups each with 2-5 markers covering a mapping distance of 7.9 to 46.4 cM. The map covers a total distance of 1027.5 cM with an average distance of 11.7 cM between two markers. The map is useful for the further development of quantitative trait loci (QTLs) affecting fruit qualities and for identification of genes conferring resistance to Fusarium wilt (races 0, 1 and 2). The present map can be used for further construction of a reference linkage map for watermelon based on an immortalized mapping population with progenies homozygous for most gene loci.

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

BMC Genomics ◽  
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.

Identification of quantitative trait loci underlying lutein content in soybean seeds across multiple environments

2017 ◽  
Vol 155 (8) ◽  
pp. 1263-1271 ◽  
Author(s):  
W. L. TENG ◽  
W. J. FENG ◽  
J. Y. ZHANG ◽  
N. XIA ◽  
J. GUO ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Phenotypic Variation ◽  
Quantitative Trait ◽  
Average Distance ◽  
Recombinant Inbred Lines ◽  
Chromosome 9 ◽  
Soybean Seeds ◽  
Trait Loci ◽  
Breeding Programmes ◽  
Lutein Content

SUMMARYLutein benefits human health significantly, including that of the eyes, skin and heart. Therefore, increasing lutein content in soybean seeds is an important objective for breeding programmes. However, no information about soybean lutein-related quantitative trait loci (QTL) has been reported, as of 2016. The aim of the present study was to identify QTLs underlying the lutein content in soybean seeds. A population including 129 recombinant inbred lines was developed from the cross between ‘Dongnong46’ (lutein 13·10 µg/g) and ‘L-100’ (lutein 23·96 µg/g), which significantly differed in seed lutein contents. This population was grown in ten environments including Harbin in 2012, 2013, 2014 and 2015; Hulan in 2013, 2014 and 2015; and Acheng in 2013, 2014 and 2015. A total of 213 simple sequence repeat markers were used to construct the genetic linkage map, which covered approximately 3623·39 cM, with an average distance of 17·01 cM between markers. In the present study, eight QTLs associated with lutein content were found initially, which could explain 1·01–19·66% of the observed phenotypic variation in ten different tested environments. The phenotypic contribution of qLU-1 (located near BARC-Satt588 on chromosome 9 (Chr 9; linkage group (LG) K)) was >10% across seven tested environments, while qLU-2 (located near Satt192 of Chr 12 (LG H)) and qLU-3 (located near Satt353 of Chr12 (LGH)) could explain 5–10% of the observed phenotypic variation in more than seven environments, respectively. qLU-5, qLU-6, qLU-7 and qLU-8 could be detected in more than four environments. These eight QTLs were novel, and have considerable potential value for marker-assistant selection of higher lutein content in soybean lines.

Sign in / Sign up

Export Citation Format

Share Document