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

Bhattarai, Gehendra; Yang, Wei; Shi, Ainong; Feng, Chunda; Dhillon, Braham; Correll, James C.; Mou, Beiquan

doi:10.1186/s12864-021-07788-8

Cited by 16 publications

(20 citation statements)

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“…Spinach is largely a dioecious crop with separate male and female plants, although some are monoecious (Morelock and Correll, 2007). The parent lines used in the crosses are often family pools of heterozygous genotypes making the linkage and QTL analysis more difficult in spinach (Bhattarai et al, 2020b). However, the GWAS approach allows us to map the trait in a mixed population or when there is a lack of fit of markers segregation for QTL mapping, as performed in this and previous spinach-downy mildew resistance mapping efforts (Bhattarai et al, 2020b;.…”

Section: Discussionmentioning

confidence: 99%

“…Before inoculation, one leaf from each labeled seedling was excised and stored for DNA extraction. Seedlings in trays were inoculated following the standard whole plant inoculation method (Feng et al, 2018b;Bhattarai et al, 2020b). Briefly, the inoculation assay involves growing plants for two weeks in the greenhouse.…”

Section: Downy Mildew Inoculation and Disease Screeningmentioning

confidence: 99%

“…Genetic mapping of the resistance sources and identification of gene-based markers are expected to facilitate R-gene pyramiding. In addition to the major R gene-based disease resistance strategy, the identification of susceptibility genes (S-genes) are being approached that may open alternative avenues to develop resistant cultivars by loss-offunction of the S-genes (Bhattarai et al, 2020b;Ribera et al, 2020). The use of the susceptibility gene in providing effective resistance are reported and established in other crop pathogen system (Bai et al, 2008;Pavan et al, 2011;Pessina et al, 2016;Wang et al, 2016a) and may be effective in providing durable and non-race-specific resistance in spinach.…”

Section: Introductionmentioning

confidence: 99%

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Mapping and selection of downy mildew resistance in spinach cv. whale by low coverage whole genome sequencing

et al. 2022

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Spinach (Spinacia oleracea) is a popular leafy vegetable crop and commercial production is centered in California and Arizona in the US. The oomycete Peronospora effusa causes the most important disease in spinach, downy mildew. A total of nineteen races of P. effusa are known, with more than 15 documented in the last three decades, and the regular emergence of new races is continually overcoming the genetic resistance to the pathogen. This study aimed to finely map the downy mildew resistance locus RPF3 in spinach, identify single nucleotide polymorphism (SNP) markers associated with the resistance, refine the candidate genes responsible for the resistance, and evaluate the prediction performance using multiple machine learning genomic prediction (GP) methods. Segregating progeny population developed from a cross of resistant cultivar Whale and susceptible cultivar Viroflay to race 5 of P. effusa was inoculated under greenhouse conditions to determine downy mildew disease response across the panel. The progeny panel and the parents were resequenced at low coverage (1x) to identify genome wide SNP markers. Association analysis was performed using disease response phenotype data and SNP markers in TASSEL, GAPIT, and GENESIS programs and mapped the race 5 resistance loci (RPF3) to 1.25 and 2.73 Mb of Monoe-Viroflay chromosome 3 with the associated SNP in the 1.25 Mb region was 0.9 Kb from the NBS-LRR gene SOV3g001250. The RPF3 locus in the 1.22-1.23 Mb region of Sp75 chromosome 3 is 2.41-3.65 Kb from the gene Spo12821 annotated as NBS-LRR disease resistance protein. This study extended our understanding of the genetic basis of downy mildew resistance in spinach cultivar Whale and mapped the RPF3 resistance loci close to the NBS-LRR gene providing a target to pursue functional validation. Three SNP markers efficiently selected resistance based on multiple genomic selection (GS) models. The results from this study have added new genomic resources, generated an informed basis of the RPF3 locus resistant to spinach downy mildew pathogen, and developed markers and prediction methods to select resistant lines.

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Section: Discussionmentioning

confidence: 99%

Section: Downy Mildew Inoculation and Disease Screeningmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Mapping and selection of downy mildew resistance in spinach cv. whale by low coverage whole genome sequencing

et al. 2022

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“…DNA extractions and sequencing details are provided in our previous publications 12 – 14 . The spinach genome of Sp75 at SpinachBase ( http://www.spinachbase.org ) was used as a reference for mapping the Illumina short reads of 201 spinach accessions using Burrows-Wheeler aligner software (BWA, 0.7.8 http://bio-bwa.sourceforge.net/) 15 .…”

Section: Methodsmentioning

confidence: 99%

Genetic dissection of nitrogen induced changes in the shoot and root biomass of spinach

Joshi

Shi

Mishra

et al. 2022

Sci Rep

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Efficient partitioning of above and below-ground biomass in response to nitrogen (N) is critical to the productivity of plants under sub-optimal conditions. It is particularly essential in vegetable crops like spinach with shallow root systems, a short growth cycle, and poor nitrogen use efficiency. In this study, we conducted a genome-wide association study (GWAS) to explore N-induced changes using spinach accessions with diverse genetic backgrounds. We evaluated phenotypic variations as percent changes in the shoot and root biomass in response to N using 201 spinach accessions grown in randomized complete blocks design in a soilless media under a controlled environment. A GWAS was performed for the percent changes in the shoot and root biomass in response to N in the 201 spinach accessions using 60,940 whole-genome resequencing generated SNPs. Three SNP markers, chr4_28292655, chr6_1531056, and chr6_37966006 on chromosomes 4 and 6, were significantly associated with %change in root weight, and two SNP markers, chr2_18480277 and chr4_47598760 on chromosomes 2 and 4, were significantly associated with % change shoot weight. The outcome of this study established a foundation for genetic studies needed to improve the partitioning of total biomass and provided a resource to identify molecular markers to enhance N uptake via marker-assisted selection or genomic selection in spinach breeding programs.

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“…Multi-parent cross populations screened with race 13 of P. effusa identified resistance-associated SNP markers located within 0.39-1.20 Mb of chromosome 3 containing the three RPF resistance loci (Bhattarai et al, 2020a). An association analysis performed on another population identified six SNP markers on chromosome 3 to be located within 0.66-1.23 Mb, providing resistance against race 16 of P. effusa (Bhattarai, 2019;Bhattarai et al, 2021b). All major resistance loci mapped so far have been detected only on the proximal end of chromosome 3.…”

Section: B Mapped Genes and Qtlsmentioning

confidence: 99%

Genomics and Marker-Assisted Improvement of Vegetable Crops

Šimko

Jia

Venkatesh

et al. 2021

Critical Reviews in Plant Sciences

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Vegetables are an integral part of the human diet worldwide. Traditional breeding approaches have been used extensively to develop new cultivars of vegetables with desirable characteristics, including resistance/tolerance to biotic and abiotic stresses, high yield, and an elevated content of compounds beneficial to human health. The technological progress since the early 1980s has revolutionized our ability to study and manipulate genetic variation in crop plants. The development of high-throughput sequencing platforms and accompanying analytical methods have led to sequencing and assembly of a large number of plant genomes, construction of dense and ultra-dense molecular linkage maps, identification of structural variants, and application of molecular markers in breeding programs. Linkage mapping and genome-wide association mapping studies have been used to identify chromosomal locations of genes and QTLs associated with plant phenotypic variations important for crop improvement. This review provides up-to-date information on the status of genomics and marker-assisted improvement of vegetable crops with the focus on tomato, pepper, eggplant, lettuce, spinach, cucumber, and chicory. For each vegetable crop, we present the most recent information on genetic resources, mapping populations, genetic maps, genome sequences, mapped genes and QTLs, the status of marker-assisted selection and genomic selection, and discuss future research prospects and application of novel techniques and approaches.

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

Cited by 16 publications

References 50 publications

Mapping and selection of downy mildew resistance in spinach cv. whale by low coverage whole genome sequencing

Mapping and selection of downy mildew resistance in spinach cv. whale by low coverage whole genome sequencing

Genetic dissection of nitrogen induced changes in the shoot and root biomass of spinach

Genomics and Marker-Assisted Improvement of Vegetable Crops

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