QTL mapping for resistance to and tolerance for the rice root-knot nematode, Meloidogyne graminicola

Galeng-Lawilao, Judith; Kumar, Arvind; Waele, Dirk De

doi:10.1186/s12863-018-0656-1

Cited by 29 publications

(26 citation statements)

References 42 publications

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“…Both QTL-seq experiments revealed segregation from 23 Mb to the bottom of chromosome 11. This locus does not seem to be close to previously detected QTLs for nematode resistance on chromosome 11 from Shrestha et al ( 2007 ) or Galeng-Lawilao et al ( 2018 ). Within this region there are 859 annotated genes (according to the Rice Genome Annotation Project) including 88 (annotated as) transposons and 167 retrotransposons, 231 “expressed protein” and 29 hypothetical genes.…”

Section: Discussioncontrasting

confidence: 63%

“…More recently, Phan et al ( 2018 ) reported a Hypersensitivity-Like Reaction (HR) to M. graminicola infection in the Asian rice cultivar Zhonghua 11 suggesting this resistance to M. graminicola to be qualitative rather than quantitative involving (a) major gene(s). Galeng-Lawilao et al ( 2018 ) have reported main effect QTLs for field resistance in Asian rice on chromosomes 4, 7 and 9 plus two epistatic interactions (between loci on chromosome 3 and 11, and between 4 and 8).…”

Section: Introductionmentioning

confidence: 99%

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QTL-seq reveals a major root-knot nematode resistance locus on chromosome 11 in rice (Oryza sativa L.)

et al. 2019

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The root-knot nematode Meloidogyne graminicola is a serious pest in rice affecting production in many rice growing areas. Natural host resistance is an attractive control strategy because the speed of the parasite’s life cycle and the broad host range it attacks make other control measures challenging. Although resistance has been found in the domesticated African rice Oryza glaberrima and the wild rice species O. longistaminata, the introgression of resistance genes to Asian rice O. sativa is challenging. Resistance due to a major gene in O. sativa would greatly aid breeding. Recently two accessions resistant to M. graminicola have been identified in a screen of 332 diverse O. sativa cultivars. In this study, these two resistant cultivars, LD 24 (an indica from Sri Lanka) and Khao Pahk Maw (an aus from Thailand), were crossed with a moderately susceptible cultivar, Vialone Nano (a temperate japonica from Italy). Approximately 175 F 2 progeny of both populations were screened for susceptibility to M. graminicola infection. Between 20 and 23 individuals with highest and lowest galls per plants were pooled to make susceptible and resistant bulks which were sequenced to conduct bulked segregant analysis using the QTL-seq method. This revealed a nematode resistance locus from 23 Mbp to the bottom of rice chromosome 11 in both crosses suggesting a rare introgression of the same locus is responsible for resistance in both cultivars. While this information can be used in marker-assisted breeding, analysis of available SNP data revealed candidate loci and genes worthy of further investigation for gene identification. Electronic supplementary material The online version of this article (10.1007/s10681-019-2427-0) contains supplementary material, which is available to authorized users.

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Section: Discussioncontrasting

confidence: 63%

Section: Introductionmentioning

confidence: 99%

QTL-seq reveals a major root-knot nematode resistance locus on chromosome 11 in rice (Oryza sativa L.)

et al. 2019

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“…However, the yield of rice is substantially afflicted by several biotrophic pathogens including rice root-knot nematode (RRKN), Meloidogyne graminicola. This sedentary endoparasite occurs in a wide range of rice-based production systems in South and Southeast Asia, including lowland, upland, rainfed, irrigated, deep-water as well as aerobic rice, and causes economic yield loss of rice [2][3][4][5][6][7]. In the vascular bundle, near the root tip, RRKN induces a feeding site (3-5 giant cells) that serves as the permanent nutrient sink for the nematode.…”

Section: Introductionmentioning

confidence: 99%

“…In order to mitigate the loss by RRKN in rice, use of chemical nematicides, crop rotation (with mung bean, mustard and sesame as poor hosts) and continuous flooding are the recommended practices [3,6,7]. Although prolonged flooding may reduce the RRKN populations by inhibiting the second-stage juveniles (J2) to invade rice roots, increasing scarcity of water for agricultural use may render this practice impractical to adopt.…”

Section: Introductionmentioning

confidence: 99%

“…Jena et al [14] reported QTLs associated with number of galls and eggs per root system on chromosomes 1 and 3 in RILs derived from the cross of O. sativa accessions 'Annapurna' and 'Ramakrishna'. Likewise, QTLs for resistance and tolerance to RRKN and other yield-contributing traits (such as root and shoot weight, plant height, % filled grains) were mapped on different chromosomal regions in RILs derived from different O. sativa accessions including 'IR64', 'IR78877-208-B-1-2' and O. glaberrima accession 'CG14' [7,9].…”

Section: Introductionmentioning

confidence: 99%

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A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola

Hada¹,

Singh²,

Singh³

et al. 2020

PLoS ONE

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Rice root-knot nematode (RRKN), Meloidogyne graminicola is one of the major biotic constraints in rice-growing countries of Southeast Asia. Host plant resistance is an environmentally-friendly and cost-effective mean to mitigate RRKN damage to rice. Considering the limited availability of genetic resources in the Asian rice (Oryza sativa) cultivars, exploration of novel sources and genetic basis of RRKN resistance is necessary. We screened 272 diverse wild rice accessions (O. nivara, O. rufipogon, O. sativa f. spontanea) to identify genotypes resistant to RRKN. We dissected the genetic basis of RRKN resistance using a genome-wide association study with SNPs (single nucleotide polymorphism) genotyped by 50K "OsSNPnks" genic Affymetrix chip. Population structure analysis revealed that these accessions were stratified into three major sub-populations. Overall, 40 resistant accessions (nematode gall number and multiplication factor/MF < 2) were identified, with 17 novel SNPs being significantly associated with phenotypic traits such as number of galls, egg masses, eggs/egg mass and MF per plant. SNPs were localized to the quantitative trait loci (QTL) on chromosome 1, 2, 3, 4, 6, 10 and 11 harboring the candidate genes including NBS-LRR, Cf2/Cf5 resistance protein, MYB, bZIP, ARF, SCARECROW and WRKY transcription factors. Expression of these identified genes was significantly (P < 0.01) upregulated in RRKN-infected plants compared to mock-inoculated plants at 7 days after inoculation. The identified SNPs enrich the repository of candidate genes for future markerassisted breeding program to alleviate the damage of RRKN in rice.

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Transgressive resistance to Heterodera glycines in chromosome segment substitution lines derived from susceptible soybean parents

Huang

Qin

et al. 2021

The Plant Genome

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Chromosome segment substitution lines (CSSLs) are valuable genetic resources for quantitative trait loci (QTL) mapping of complex agronomic traits especially suitable for minor effect QTL. Here, 162 BC 3 F 7 -BC 7 F 3 CSSLs derived from crossing two susceptible parent lines, soybean [Glycine max (L.) Merr.] 'Suinong14' (recurrent parent) × wild soybean (G. soja Siebold & Zucc.) ZYD00006, were used for QTL mapping of soybean cyst nematode (SCN, Heterodera glycine Ichinohe) resistance based on female index (FI) and cysts per gram root (CGR) through phenotypic screening and whole-genome resequencing of CSSLs. Phenotypic results displayed a wide range of distribution and transgressive lines in both HG Type 2.5.7 FI and CGR and demonstrated a higher correlation between CGR and root weight (R 2 = .5424) compared with than between FI and CGR (R 2 = .0018). Using the singlemarker analysis nonparametric mapping test, 33 significant QTL were detected on 18 chromosomes contributing resistance to FI and CGR. Fourteen QTL contributing 5.6-15.5% phenotypic variance (PVE) to FI were revealed on 11 chromosomes, and 16 QTL accounting for 6.1-36.2% PVE in CGR were detected on 14 chromosomes with strong additive effect by multiple-QTL model (MQM) mapping. Twenty-five and 13 out of all 38 QTL identified for FI and CGR on 20 chromosomes were from

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QTL mapping for resistance to and tolerance for the rice root-knot nematode, Meloidogyne graminicola

Cited by 29 publications

References 42 publications

QTL-seq reveals a major root-knot nematode resistance locus on chromosome 11 in rice (Oryza sativa L.)

QTL-seq reveals a major root-knot nematode resistance locus on chromosome 11 in rice (Oryza sativa L.)

A genome-wide association study in Indian wild rice accessions for resistance to the root-knot nematode Meloidogyne graminicola

Transgressive resistance to Heterodera glycines in chromosome segment substitution lines derived from susceptible soybean parents

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