Dataset Information

Fine Mapping of a Resistance Gene RpsHN that Controls Phytophthora sojae Using Recombinant Inbred Lines and Secondary Populations.

ABSTRACT: Phytophthora root rot (PRR), caused by Phytophthora sojae, has negative effects on soybean yield in China and can be controlled by identifying germplasm resources with resistance genes. In this study, the resistance locus RpsHN in the soybean line Meng8206 was mapped using two mapping populations. Initial mapping was realized using two recombinant inbred line (RIL) populations and included 103 F6:8 RILs derived from a cross of Meng8206 × Linhedafenqing, including 2600 bin markers, and 130 F6:8 RILs derived from a cross of Meng8206 × Zhengyang148, including 2267 bin markers. Subsequently, a 159 F2:3 secondary population derived from a cross of Meng8206 × Linmeng6-46, were used to fine map this locus using SSR markers. Finally, the resistance locus from Meng8206 was fine mapped to a 278.7 kb genomic region flanked by SSR markers SSRSOYN-25 and SSRSOYN-44 at a genetic distance of 1.6 and 1.0 cM on chromosome 3 (Chr. 03). Real-time RT-PCR analysis of the possible candidate genes showed that three genes (Glyma.03g04260, Glyma.03g04300, and Glyma.03g04340) are likely involved in PRR resistance. These results will serve as a basis for cloning, transferring of resistant genes and breeding of P. sojae-resistant soybean cultivars through marker-assisted selection.

SUBMITTER: Niu J

PROVIDER: S-EPMC5387331 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Fine Mapping of a Resistance Gene RpsHN that Controls Phytophthora sojae Using Recombinant Inbred Lines and Secondary Populations.

Niu Jingping J Guo Na N Sun Jutao J Li Lihong L Cao Yongce Y Li Shuguang S Huang Jianli J Zhao Jinming J Zhao Tuanjie T Xing Han H

Frontiers in plant science 20170411

Phytophthora root rot (PRR), caused by Phytophthora sojae, has negative effects on soybean yield in China and can be controlled by identifying germplasm resources with resistance genes. In this study, the resistance locus RpsHN in the soybean line Meng8206 was mapped using two mapping populations. Initial mapping was realized using two recombinant inbred line (RIL) populations and included 103 F6:8 RILs derived from a cross of Meng8206 × Linhedafenqing, including 2600 bi ...[more]

PMID: 28443124

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Project description:Phytophthora root and stem rot caused by the oomycete pathogen Phytophthora sojae, is one of the most destructive diseases of soybean. Deploying soybean cultivars carrying race-specific resistance conferred by Rps genes is the most practicalapproach to managing this disease. Previously, two Rps genes, RpsUN1 and RpsUN2 conferring broad spectra of resistance to P. sojae isolates, were identified in a landrace PI 567139B and mapped to a 6.5-cM region on chromosome 3 and a 3.0-cM region on chromosome 16, corresponding to 840 kb and 600 kb of sequences, respectively,of the soybean reference genome. By analyzing ten and nine recombinants defined by genotypic and phenotypic screening of the 826 F2:3 families derived from two reciprocal crosses between the two parental lines of the mapping populations, RpsUN1 and RpsUN2 were further narrowed to a 151-kb region that harbors five genes including three NBS-LRR genes, and a 36-kb region that contains four genes including five NBS-LRR genes, respectively, according to the reference genome. Analysis of expressional changes of these nine genes before and after inoculation with the pathogen suggest that the counterparts of Glyma.03g034600 in the RpsUN1 region and the counterparts of Glyma.16g215200 and Glyma.16g214900 in the RpsUN2 region of PI 567139B may be associated with the resistance to P. sojae. It is also suggested that unequal recombination between different NBS-LRR genes in the mapped regions may have occurred, resulting in the formation of two recombinants with inconsistent genotypes and phenotypes detected by molecular markers within the fine-mapped regions. The haplotypes of genomic regions surrounding RpsUN1 and RpsUN2 in the entire soybean germplasm deposited in the US soybean germplasm collection were analyzed towards a better understanding of the origins of these two novel sources of resistance and screening of effective markers for marker-assisted selectionof these two resistance genes for soybean breeding.

Project description:Recombinant inbred (RI) strains are an important resource for mapping complex traits in many species. While large RI panels are available for Arabidopsis, maize, C. elegans, and Drosophila, mouse RI panels typically consist of fewer than 30 lines. This is a severe constraint on the power and precision of mapping efforts and greatly hampers analysis of epistatic interactions.In order to address these limitations and to provide the community with a more effective collaborative RI mapping panel we generated new BXD RI strains from two independent advanced intercrosses (AI) between C57BL/6J (B6) and DBA/2J (D2) progenitor strains. Progeny were intercrossed for 9 to 14 generations before initiating inbreeding, which is still ongoing for some strains. Since this AI base population is highly recombinant, the 46 advanced recombinant inbred (ARI) strains incorporate approximately twice as many recombinations as standard RI strains, a fraction of which are inevitably shared by descent. When combined with the existing BXD RI strains, the merged BXD strain set triples the number of previously available unique recombinations and quadruples the total number of recombinations in the BXD background.The combined BXD strain set is the largest mouse RI mapping panel. It is a powerful tool for collaborative analysis of quantitative traits and gene function that will be especially useful to study variation in transcriptome and proteome data sets under multiple environments. Additional strains also extend the value of the extensive phenotypic characterization of the previously available strains. A final advantage of expanding the BXD strain set is that both progenitors have been sequenced, and approximately 1.8 million SNPs have been characterized. This provides unprecedented power in screening candidate genes and can reduce the effective length of QTL intervals. It also makes it possible to reverse standard mapping strategies and to explore downstream effects of known sequence variants.

Project description:Soybean (Glycine max (L.) Merr.) isoflavone is important for human health and plant defense system. To identify novel quantitative trait loci (QTL) and epistatic QTL underlying isoflavone content in soybean, F5:6, F5:7 and F5:8 populations of 130 recombinant inbred (RI) lines, derived from the cross of soybean cultivar 'Zhong Dou 27' (high isoflavone) and 'Jiu Nong 20' (low isoflavone), were analyzed with 95 new SSR markers. A new linkage map including 194 SSR markers and covering 2,312 cM with mean distance of about 12 cM between markers was constructed. Thirty four QTL for both individual and total seed isoflavone contents of soybean were identified. Six, seven, ten and eleven QTL were associated with daidzein (DZ), glycitein (GC), genistein (GT) and total isoflavone (TI), respectively. Of them 23 QTL were newly identified. The qTIF_1 between Satt423 and Satt569 shared the same marker Satt569 with qDZF_2, qGTF_1 and qTIF_2. The qGTD2_1 between Satt186 and Satt226 was detected in four environments and explained 3.41%-10.98% of the phenotypic variation. The qGTA2_1, overlapped with qGCA2_1 and detected in four environments, was close to the previously identified major QTL for GT, which were responsible for large a effects. QTL (qDZF_2, qGTF_1 and qTIF_2) between Satt144-Satt569 were either clustered or pleiotropic. The qGCM_1, qGTM_1 and qTIM_1 between Satt540-Sat_244 explained 2.02%-9.12% of the phenotypic variation over six environments. Moreover, the qGCE_1 overlapped with qGTE_1 and qTIE_1, the qTIH_2 overlapped with qGTH_1, qGCI_1 overlapped with qDZI_1, qTIL_1 overlapped with qGTL_1, and qTIO_1 overlapped with qGTO_1. In this study, some of unstable QTL were detected in different environments, which were due to weak expression of QTL, QTL by environment interaction in the opposite direction to a effects, and/or epistasis. The markers identified in multi-environments in this study could be applied in the selection of soybean cultivars for higher isoflavone content and in the map-based gene cloning.

Dataset Information

Fine Mapping of a Resistance Gene RpsHN that Controls Phytophthora sojae Using Recombinant Inbred Lines and Secondary Populations.

Publications

Fine Mapping of a Resistance Gene <i>RpsHN</i> that Controls <i>Phytophthora sojae</i> Using Recombinant Inbred Lines and Secondary Populations.

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