Genome-wide association mapping reveals genomic regions frequently associated with lettuce field resistance to downy mildew

Šimko, Ivan; Peng, Hui; Kandel, Jinita Sthapit; Zhao, Rebecca

doi:10.1007/s00122-022-04090-3

Cited by 12 publications

(9 citation statements)

References 43 publications

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“…In the 3 reference assemblies, we annotated repeat elements and classified them into TEs and other repeats ( Supplementary Data 3a ). The genomes of all 3 Lactuca species contained a major proportion of TEs, in agreement with previous studies ( Supplementary Table 6 ) ( Simko et al 2022 ). Unsurprisingly, the TE content of the L. virosa (60%) assembly is proportionally lower than that of both L. sativa (74%) and L. saligna (77%), which is likely caused by an incomplete search due to the high N content in the L. virosa assembly.…”

Section: Resultssupporting

confidence: 91%

“…A reference genome and derived molecular markers are essential for breeders to select traits accurately and trace introgressions in cultivated lettuce from L. virosa . For example, genome-wide association studies (GWAS) have been performed to identify SNP variants ( Mikel 2013 ) that are associated with interesting traits in lettuce ( Walley et al 2017 ; Sthapit Kandel et al 2020 ; Simko et al 2022 ) using the assembled lettuce ( L. sativa ) reference genome ( Reyes-Chin-Wo et al 2017 ), which can be used to develop markers for lettuce breeding to accelerate selection in offspring ( Simko 2013 ). In addition to GWAS, a reference genome of L. virosa will also facilitate genomic analyses for various biological questions.…”

Section: Introductionmentioning

confidence: 99%

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Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

Xiong,

van Workum,

Berke

et al. 2023

G3: Genes, Genomes, Genetics

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Lettuce (Lactuca sativa L.) is a leafy vegetable crop with ongoing breeding efforts related to quality, resilience, and innovative production systems. To breed resilient and resistant lettuce in the future, valuable genetic variation found in close relatives could be further exploited. Lactuca virosa (2x=2n=18), a wild relative assigned to the tertiary lettuce gene pool, has a much larger genome (3.7 Gbp) than Lactuca sativa (2.5 Gbp). It has been used in interspecific crosses and is a donor to modern crisphead lettuce cultivars. Here, we present a de novo reference assembly of L. virosa with high continuity and complete gene space. This assembly facilitated comparisons to the genome of L. sativa and to that of the wild species L. saligna, a representative of the secondary lettuce gene pool. To assess the diversity in gene content, we classified the genes of the three Lactuca species as core, accessory and unique. In addition, we identified three interspecific chromosomal inversions compared to L. sativa, which each may cause recombination suppression and thus hamper future introgression breeding. Using three-way comparisons in both reference-based and reference-free manners, we show that the proliferation of long-terminal repeat elements has driven the genome expansion of L. virosa. Further, we performed a genome-wide comparison of immune genes, nucleotide-binding leucine-rich repeat, and receptor-like kinases among Lactuca spp. and indicate the evolutionary patterns and mechanisms behind their expansions. These genome analyses greatly facilitate the understanding of genetic variation in L. virosa, which is beneficial for the breeding of improved lettuce varieties.

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Section: Resultssupporting

confidence: 91%

Section: Introductionmentioning

confidence: 99%

Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

Xiong,

van Workum,

Berke

et al. 2023

G3: Genes, Genomes, Genetics

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“…Previously performed analyses of population structure revealed a possible presence of three main subgroups within the diversity panel, with a potential further division into six to eight subgroups ( Sthapit Kandel et al., 2020 ; Peng et al., 2022 ; Simko et al., 2022a ). GWAS analysis carried out on SPAD-Sqrt and ACI-Lb data revealed four QTLs associated with the content of chlorophyll and 12 QTLs for anthocyanins ( Table 3 ).…”

Section: Resultsmentioning

confidence: 99%

“…In addition, two accessions of L. indica were included in the diversity panel for a phenotypic comparison but were not used in the GWAS. This diversity set was described in detail in previous studies that focused on mapping quantitative trait loci (QTLs) for plant development, postharvest quality ( Sthapit Kandel et al., 2020 ), and resistance to yellow spot malady ( Peng et al., 2022 ), downy mildew ( Simko et al., 2022a ) and bacterial leaf spot ( Sthapit Kandel et al., 2022 ). Two biparental mapping populations used for linkage mapping consisted of 88 (GR × Sal) and 160 (Ice × PI) F 7 recombinant inbred lines (RILs).…”

Section: Methodsmentioning

confidence: 99%

Genetic and physiological determinants of lettuce partial resistance to Impatiens necrotic spot virus

Šimko¹,

Hasegawa²,

Peng³

et al. 2023

Front. Plant Sci.

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IntroductionImpatiens necrotic spot virus (INSV) is a major pathogen currently threatening lettuce (Lactuca sativa L.) production in the coastal areas of California. The virus is transmitted by the western flower thrips (Frankliniella occidentalis Pergande).MethodsWe have tested a diversity panel of almost 500 lettuce accessions for disease incidence (DI) in 12 field experiments performed over 7 years. This set of accessions was also assessed for thrips feeding damage (TFD), the rate of plant development (PD), and the content of chlorophyll (SPAD) and anthocyanins (ACI) to determine their effect on resistance to INSV. In addition, recombinant inbred lines from two biparental mapping populations were also evaluated for DI in field experiments.ResultsThe mean DI in 14 field experiments ranged from 2.1% to 70.4%. A highly significant difference in DI was observed among the tested accessions, with the overall lowest DI detected in the red color cultivars, Outredgeous Selection, Red Splash Cos, Infantry, Sweet Valentine, Annapolis, and Velvet. Multiple linear regression models revealed a small but significant effect (p < 0.005) of the four analyzed determinants on DI. Accessions with lower DI values had slower plant development (PD, r = 0.352), higher ACI content (r = −0.284), lower TFD (r = 0.198), and lower SPAD content (r = 0.125). A genome-wide association study revealed 13 QTLs for DI located on eight out of the nine lettuce chromosomes (the exception was chr. 8). The most frequently detected QTL (qINSV2.1) was located on chr. 2. Several of the QTLs for DI were in the same genomic areas as QTLs for PD, ACI, and SPAD. Additional three QTLs for DI on chr. 5 and 8 were identified using linkage mapping performed on two biparental mapping populations.ConclusionsThe work highlights the genetic basis of partial resistance to INSV and reveals the relationship between resistance, the host physiology, and the thrips vector. Results of this study are an important steppingstone toward developing cultivars with increased resistance against INSV.

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“…The main objective for generating tGBS markers using the diversity panel of ∼500 lettuce accessions was to apply genome-wide association studies (GWAS) to map quantitative trait loci (QTL) for resistance to Impatiens necrotic spot virus (INSV) [3] , downy mildew [4] bacterial leaf spot [5] , lettuce drop, yellow spot malady [6] , plant development, postharvest quality [7] , content of anthocyanins and chlorophylls, and other economically important traits. Seeds of genotyped accessions are available for distribution to collaborators.…”

Section: Objectivementioning

confidence: 99%

Genome-wide association mapping reveals genomic regions frequently associated with lettuce field resistance to downy mildew

Cited by 12 publications

References 43 publications

Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

Genetic and physiological determinants of lettuce partial resistance to Impatiens necrotic spot virus

Dataset on the single nucleotide variation in diversity panel of 500 lettuce accessions genotyped with tunable genotyping-by-sequencing (tGBS) method

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