Research advances and prospects of spinach breeding, genetics, and genomics

Bhattarai, Gehendra; Shi, Ainong

doi:10.48130/vr-2021-0009

Cited by 21 publications

(22 citation statements)

References 126 publications

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“…Similar approaches have been tested for many traits in several crops and found it practical to do genome breeding using GWAS-derived SNP markers [ 49 – 51 , 53 , 72 ]. Therefore, GP approach combining both MAS and GS through GEBVs using associated SNP markers would be valuable in molecular breeding for white rust resistance in spinach and for other quantitative traits in other plant species, and assessment of genomic prediction potential is ongoing on several important traits in spinach [ 74 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN spinach germplasm

Shi

Bhattarai

Xiong

et al. 2022

Horticulture Research

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White rust, caused by Albugo occidentalis, is one of the major yield-limiting diseases of spinach (Spinacia oleracea) in some major commercial production areas, particularly in southern Texas in the United States. The use of host resistance is the most economical and environment-friendly approach to managing white rust in spinach production. The objectives of this study were to conduct a genome-wide associating study (GWAS), to identify single nucleotide polymorphism (SNP) markers associated with white rust resistance in spinach, and to perform genomic prediction (GP) to estimate the prediction accuracy (PA). A GWAS panel of 346 USDA (US Dept. of Agriculture) germplasm accessions was phenotyped for white rust resistance under field conditions and GWAS was performed using 13 235 whole-genome resequencing (WGR) generated SNPs. Nine SNPs, chr2_53 049 132, chr3_58 479 501, chr3_95 114 909, chr4_9 176 069, chr4_17 807 168, chr4_83 938 338, chr4_87 601 768, chr6_1 877 096, and chr6_31 287 118, located on chromosomes 2, 3, 4, and 6 were associated with white rust resistance in this GWAS panel. Four scenarios were tested for PA using Pearson’s correlation coefficient (r) between the genomic estimation breeding value (GEBV) and the observed values: (1) different ratios between the training set and testing set (fold), (2) different GP models, (3) different SNP numbers in three different SNP sets, and (4) the use of GWAS-derived significant SNP markers. The results indicated a 2- to 10-fold difference in the various GP models had similar, although not identical, averaged r values in each SNP set; using GWAS-derived significant SNP markers would increase PA with a high r-value up to 0.84. The SNP markers and the high PA can provide valuable information for breeders to improve spinach by marker-assisted selection (MAS) and genomic selection (GS).

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Section: Discussionmentioning

confidence: 99%

Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN spinach germplasm

Shi

Bhattarai

Xiong

et al. 2022

Horticulture Research

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“…Downy mildew is the major disease in commercial spinach production worldwide and in the United States, as the infected leaves are unmarketable. Spinach hybrid cultivars combining RPF alleles effective against multiple races of P. effusa from two parents are available ( Correll et al., 2011 ; Bhattarai and Shi, 2021 ). However, new races of downy mildew pathogens are emerging and are overcoming the genetic resistance deployed in the new cultivars.…”

Section: Discussionmentioning

confidence: 99%

“…The objective was to compare multiple machine learning models and the influence of a different set of markers in the prediction performance of downy mildew race-specific resistance in spinach. GS has recently been evaluated in spinach for resistance to white rust ( Shi et al., 2022 ), field evaluated downy mildew ( Bhattarai et al., 2022 ), while some other phenotypes are being assessed for GP in spinach ( Bhattarai and Shi, 2021 ). Five GP models involving parametric models (rrBLUP, BB, BL, and BRR) and nonparametric models (SVM) in four marker datasets provide a comparative advantage between models and marker sets.…”

Section: Discussionmentioning

confidence: 99%

“…Downy mildew, caused by the obligate oomycete Peronospora effusa , is the most economically important disease of spinach, making the produce unmarketable after infection. Breeding for resistance to downy mildew pathogen is the primary objective of all spinach breeding programs ( Morelock and Correll, 2007 ; Bhattarai and Shi, 2021 ). Nineteen unique races of P. effusa have been documented ( Feng et al., 2014 ; Feng et al., 2018b ; Plantum, 2021 ) in spinach, of which sixteen were reported in the last three decades.…”

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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“…Spinach is easily influenced by the photoperiod ( Chun et al, 2000b ), and bolts in spring ( Tang et al, 2018 ). New slow-bolting spinach cultivars available to that can adapt to a wide range of photoperiods and climatic conditions ( Bhattarai and Shi, 2021 ). Selecting the appropriate cultivars will improve the efficiency of breeding and production in spinach ( Goreta and Leskovar, 2006 ).…”

Section: Introductionmentioning

confidence: 99%

Quantitative Trait Locus Mapping and Identification of Candidate Genes Controlling Bolting in Spinach (Spinacia oleracea L.)

Liu

Feng²,

Zhang

et al. 2022

Front. Plant Sci.

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Spinach is a typical light-sensitive plant. Long days can induce early bolting, thereby influencing the regional adaptation, quality, and vegetative yield of spinach. However, the genes and genetic mechanisms underlying this trait in spinach remain unclear. In this study, a major quantitative trait locus (QTL) qBT1.1, was mapped on chromosome 1 using a BC1 population (BC1a) derived from 12S3 (late-bolting recurrent lines) and 12S4 (early bolting lines) with specific-locus amplified fragment (SLAF) markers and Kompetitive Allele Specific PCR (KASP) markers. The qBT1.1 locus was further confirmed and narrowed down to 0.56 Mb by using a large BC1 (BC1b) population and an F2 population using the above KASP markers and the other 20 KASP markers. Within this region, two putative genes, namely, SpFLC and SpCOL14, were of interest due to their relationship with flower regulatory pathways. For SpCOL14, we found multiple variations in the promoter, and the expression pattern was consistent with bolting stages. SpCOL14 was therefore assumed to the best candidate gene for bolting. Overall, our results provide a basis for understanding the molecular mechanisms of bolting in spinach and contribute to the breeding of diverse spinach germplasms for adaptation to different regions.

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Research advances and prospects of spinach breeding, genetics, and genomics

Cited by 21 publications

References 126 publications

Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN spinach germplasm

Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN spinach germplasm

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

Quantitative Trait Locus Mapping and Identification of Candidate Genes Controlling Bolting in Spinach (Spinacia oleracea L.)

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