Pinpointing genes underlying the quantitative trait loci for root-knot nematode resistance in palaeopolyploid soybean by whole genome resequencing

Xu, Xiangyang; Zeng, Liang; Tao, Ye; Vuong, Tri D.; Wan, Jinrong; Boerma, Roger; Noe, J. P.; Li, Zenglu; Finnerty, Steve; Pathan, Safiullah; Shannon, J. Grover; Nguyen, Henry T.

doi:10.1073/pnas.1222368110

Cited by 111 publications

(118 citation statements)

References 33 publications

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“…irregulare and F. graminearum (Glazebrook, 2005;Kou and Wang, 2010;Kou and Wang, 2012). Prior to cloning genes from resistant genotypes associated with quantitative disease resistance in plants, characterizing the type of resistance, identifying and mapping the loci, and narrowing the locus requires a population that is both advanced in generation and large in size to capture the greatest number of recombination events (St. Clair, 2010;Xu et al, 2013). There have been several advancements in this arena where genes associated with quantitative resistance have been cloned and identified.…”

Section: Discussionmentioning

confidence: 99%

High‐Density Mapping of Resistance QTL Toward Phytophthora sojae, Pythium irregulare, and Fusarium graminearum in the Same Soybean Population

et al. 2016

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Phytophthora sojae Kaufm. and Gerd., Pythium irregulare Busiman, and Fusarium graminearum Schwabe [teleomorph: Gibberella zeae (Schwien.) Petch] are important pathogens of soybean [Glycine max (L.) Merr.] and are all capable of causing seed rot, damping‐off, and root rot. The objective of this study was to identify quantitative trait loci (QTL) for resistance to Py. irregulare and to refine previously mapped QTL for resistance to P. sojae and F. graminearum in a larger, more advanced ‘Conrad’ × ‘Sloan’ F9:11 recombinant inbred line population. The population was mapped with 1032 single nucleotide polymorphisms from the SoySNP6K BeadChip and 31 polymerase chain reaction–based molecular markers. Families were evaluated for resistance response to three isolates of P. sojae, one isolate of Py. irregulare, and one isolate of F. graminearum. A total of 10, 2, and 3 QTL and suggestive QTL were found that confer resistance to P. sojae, Py. irregulare, and F. graminearum, respectively. Individual QTL explained 2 to 13.6% of the phenotypic variance. Quantitative trait loci for resistance toward both Py. irregulare and F. graminearum colocalized on chromosome 19. This resistance was contributed by Sloan and was juxtaposed to a QTL for P. sojae with resistance contributed from Conrad. Alleles for resistance to different pathogens contributed from different parents in the same region; the number of unique QTL for each pathogen and the lack of correlation of resistance suggest that different mechanisms are involved in resistance toward P. sojae, Py. irregulare, and F. graminearum.

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Section: Discussionmentioning

confidence: 99%

High‐Density Mapping of Resistance QTL Toward Phytophthora sojae, Pythium irregulare, and Fusarium graminearum in the Same Soybean Population

et al. 2016

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“…Three QTLs underlying RKN resistance in PI438489B, were identified on Chrs. 8, 10, and 13 (Xu et al 2013). Ibrahim et al (2011) identified that silencing of tyrosine phosphatase (TP) and mitochondrial stress-70 protein precursor (MSP) genes can decrease gall formation of RKN.…”

Section: Discussionmentioning

confidence: 99%

Reaction of Soybean Cyst Nematode Resistant Plant Introductions to Root-Knot and Reniform Nematodes

Lee¹,

Kim²,

Robbins³

et al. 2015

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Out of these accessions, 64 PIs were identified with high or moderate resistance to RKN. Of these 64 lines, 24 accessions showed good resistance to both RKN and RN. These new sources of resistance to multiple nematodes will be valuable materials for soybean breeding programs to develop new resistant cultivars that can overcome yield losses caused by one or more of these nematode species.

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“…The 50 Chinese lines represented wild soybean, land races, and elite cultivars allowing the researchers to differentiate between candidate genes associated with soybean domestication and improvement. Xu et al (2013) used genome re-sequencing approaches to generate and validate SNPs that were used for QTL mapping of root-knot nematode resistance. Their approach identified two candidate genes responsible for resistance.…”

Section: Applications For Mirna In Soybean Functional Genomicsmentioning

confidence: 99%

Soybean Functional Genomics: Bridging the Genotype-to-Phenotype Gap

O’Rourke

Graham

Whitham

2017

Compendium of Plant Genomes

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Technological advances coupled with the economic importance of soybean have led to increased efforts to understand gene function and associate genes with phenotypes of agronomic and fundamental interest. Functional genomics approaches aim to develop sufficient understanding needed to bridge the genotype-tophenotype gap. In general terms, functional genomics approaches begin by using highly parallelized methods to analyze genomes, transcriptomes, proteomes, and metabolomes to generate hypotheses about genes that control phenotypes. Candidate genes are then tested for their contributions to phenotypes through various methods such as RNA silencing, genetic mutation, or overexpression. In this chapter, we review the current approaches, tools, and resources that are being applied for functional genomics research in soybean. RightsWorks produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted. Technological advances coupled with the economic importance of soybean have led to increased efforts to understand gene function and associate genes with phenotypes of agronomic and fundamental interest. Functional genomics approaches aim to develop sufficient understanding needed to bridge the genotype-to-phenotype gap. In general terms, functional genomics approaches begin by using highly parallelized methods to analyze genomes, transcriptomes, proteomes, and metabolomes to generate hypotheses about genes that control phenotypes. Candidate genes are then tested for their contributions to phenotypes through various methods such as RNA silencing, genetic mutation, or overexpression. In this chapter, we review the current approaches, tools, and resources that are being applied for functional genomics research in soybean.

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Pinpointing genes underlying the quantitative trait loci for root-knot nematode resistance in palaeopolyploid soybean by whole genome resequencing

Cited by 111 publications

References 33 publications

High‐Density Mapping of Resistance QTL Toward Phytophthora sojae, Pythium irregulare, and Fusarium graminearum in the Same Soybean Population

High‐Density Mapping of Resistance QTL Toward Phytophthora sojae, Pythium irregulare, and Fusarium graminearum in the Same Soybean Population

Reaction of Soybean Cyst Nematode Resistant Plant Introductions to Root-Knot and Reniform Nematodes

Soybean Functional Genomics: Bridging the Genotype-to-Phenotype Gap

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