Identification and mapping of quantitative trait loci associated with soybean rust (Phakopsora pachyrhizi) resistance in genotype UG 5

Gebremedhn, Hailay Mehari; Msiska, Ulemu Mercy; Weldekidan, Miesho Belay; Asmamaw, Fentaw Abate; Winnifred, Akech; Onziga, Dramadri Isaac; Odong, Thomas; Rubaihayo, Patrick; Tukamuhabwa, Phinehas

doi:10.5897/ajb2018.16661

Cited by 5 publications

(3 citation statements)

References 31 publications

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“…Microsatellite markers are one of the most efficient types of molecular markers because of their high polymorphism, wide genome coverage, co-dominant inheritance, and good reproducibility (Powell et al, 1996;Gupta and Varshney, 2000;Varshney et al, 2005). Hence, they have been widely used in genetic linkage map, quantitative trait loci (QTL) mapping, marker-assisted selection (MAS) breeding, evolutionary studies, and genetic diversity analysis (Nishio et al, 2008;Garvin et al, 2010;Ahmadi and Fotokian, 2011;Wang et al, 2015;Zhao et al, 2019). Traditional methods for developing microsatellite markers are time-consuming, laborious, and expensive (Zane et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing

Wang

et al. 2020

Front. Genet.

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Pseudotaxus chienii (Taxaceae) is an endangered conifer species endemic to China. However, a lack of suitable molecular markers hinders the genomic and genetic studies on this species. Here, we characterized and developed the microsatellite markers from a newly sequenced P. chienii transcriptome. A total of 21,835 microsatellite loci were detected from 161,131 non-redundant unigene sequences, and the frequency of SSRs was 13.55%, with an average of one SSR loci per 9.18 kb. Mono-nucleotide, dinucleotide, and tri-nucleotide were the dominant repeat types, accounting for 50.06, 13.49, and 29.39% of the total SSRs, respectively. In terms of distribution location, the coding regions (CDS) with few microsatellites and mainly consisted of tri-nucleotides. There were significant differences in the length of microsatellite among genic regions and motif types. Functional annotation showed that the unigenes containing microsatellites had a wide range of biological functions, most of which were related to basic metabolism, and a few might be involved in expression regulation of gene and response to environmental stress. In addition, 375 primer pairs were randomly selected and synthesized for the amplification and validation of microsatellite markers. Seventyseven primer pairs were successfully amplified and 40 primer pairs were found to be polymorphic. Finally, 20 pairs of primers with high polymorphism were selected to assess the genetic diversity in four P. chienii populations. In addition, the newly developed microsatellite markers exhibited high transferability (70%) in Amentotaxus argotaenia. Our study could enable further genetic diversity analysis and functional gene mining on Taxaceae.

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Section: Introductionmentioning

confidence: 99%

Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing

Wang

et al. 2020

Front. Genet.

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“…Genomic DNA was extracted from young leaves of the parental genotypes and 86 individual F 2 plants using CTAB (Lemos et al, 2011). After checking the purity and concentration of the DNA samples, screening was made using PCR with a total of 122 SSR markers (Hailay et al, 2018). Of the 33 polymorphic SSR markers obtained using QTL IciMapping 4.1 software, 13 SSR markers which were associated with the identified QTLs were used to genotype the F 2 progenies (Hailay et al, 2018).…”

Section: Methodsmentioning

confidence: 99%

“…After checking the purity and concentration of the DNA samples, screening was made using PCR with a total of 122 SSR markers (Hailay et al, 2018). Of the 33 polymorphic SSR markers obtained using QTL IciMapping 4.1 software, 13 SSR markers which were associated with the identified QTLs were used to genotype the F 2 progenies (Hailay et al, 2018). The phenotypic and genotypic data were deployed to map the putative QTLs using MapQTL version 4.0 software (Van Ooijen, 2009).…”

Section: Methodsmentioning

confidence: 99%

Prediction of candidate genes associated with resistance to soybean rust (Phakopsora pachyrhizi) in line UG‐5

et al. 2020

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Online databases containing genetic information are crucial to extract new candidate genes from existing data and web‐based resources. The objective of this study was, therefore, to predict putative candidate genes associated with resistance to SBR in line UG‐5 and understand their functions using different bioinformatics tools from the online available databases. The physical positions for the flanking markers of the identified putative QTLs were searched on the SoyBase database genome browser based on Glyma 1.01 assembly. The putative candidate genes and annotated functions of the surrounding genes were discovered in the vicinity using SoyBase and Phytozome databases. A total of 18 putative candidate genes were predicted on approximately 482.7 kb region of QTL‐3 (chromosome 18), among which, six putative candidate genes were found to encode leucine‐rich repeat (LRR), Ser/Thr protein phosphatase, leucine‐rich repeat receptor‐like protein kinase (LRR‐RLK) and chitinase‐related proteins, which are associated with plant defence signalling pathways. Moreover, F‐box and leucine‐rich repeat, glycosyltransferase family member and serine/threonine‐protein phosphatase 2A catalytic subunit coding genes were predicted on the novel putative QTL detected on chromosome 9. This information could, therefore, be used for further prediction and annotation of candidate genes from sequenced regions of line UG‐5 as these putative candidate genes were predicted from the Glyma 1.01 assembly.

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Mapping of a soybean rust resistance in PI 594756 at the Rpp1 locus

Barros

Avelino²,

Silva³

et al. 2023

Mol Breeding

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Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi, is the main disease affecting soybean production in Brazil. The plant introduction PI 594756 is a resistance source that has been employed in breeding for resistance to ASR in this country. This study aimed at investigating the resistance of the PI 594756 to a panel of P. pachyrhizi isolates and mapping its resistance in populations derived from the cross with the susceptible PI 594891. The PI 594756 and resistant varieties were inoculated with seven ASR monosporic isolates. F 2 and F 2:3 populations were tested against ASR in a greenhouse and used to map a resistance gene to a likely genomic location by means of bulked segregant analysis. Bulks were genotyped with In nium BeadChips and the genomic region identi ed was saturated with target GBS (tGBS). PI 594756 presented a unique resistance pro le compared to the differential varieties, being resistant to six isolates and immune to one. The resistance was visually monogenic dominant; however, it was classi ed as incompletely dominant when quantitatively studied. Genetic and QTL mapping placed the PI 594756 gene between chromosome (chr) 18 55, 863,741 and 56,123,516. This position is slightly upstream mapping positionsof Rpp1 (PI 200492) and Rpp1-b (PI 594538A). Finally, we performed a haplotype analysis of a panel composed of Brazilian historical germplasm, sources of Rpp genes and resistant varieties and found SNPs that can successfully differentiated the new allele from PI 594756 from Rpp1 and Rpp1-b sources. The haplotype identi ed can be used as a tool for marker assisted selection.

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Identification and mapping of quantitative trait loci associated with soybean rust (Phakopsora pachyrhizi) resistance in genotype UG 5

Cited by 5 publications

References 31 publications

Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing

Characterization and Development of Microsatellite Markers in Pseudotaxus chienii (Taxaceae) Based on Transcriptome Sequencing

Prediction of candidate genes associated with resistance to soybean rust (Phakopsora pachyrhizi) in line UG‐5

Mapping of a soybean rust resistance in PI 594756 at the Rpp1 locus

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