Molecularly tagged genes and quantitative trait loci in cucumber with recommendations for QTL nomenclature

Wang, Yuhui; Bo, Kailiang; Gu, Xingfang; Pan, Junsong; Li, Yuhong; Chen, Jinfeng; Wen, Changlong; Ren, Zhonghai; Ren, Huazhong; Chen, Xuehao; Grumet, Rebecca; Weng, Yiqun

doi:10.1038/s41438-019-0226-3

Cited by 82 publications

(72 citation statements)

References 105 publications

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“…The detected locus was named in accordance with the following scheme: the abbreviation of HT, chromosome (Chr.) number, and locus number [35]. Since the preliminary mapping region was still large, polymorphic Indel markers were used to narrow down the region.…”

Section: Qtl Mapping Of Heat Tolerancementioning

confidence: 99%

QTL Mapping of Heat Tolerance in Cucumber (Cucumis sativus L.) at Adult Stage

Liu

Dong

Wei

et al. 2021

Plants

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Heat stress during cucumber production often leads to sunburn of leaves, growth retardation of stems and roots, fruit malformation, and even plant death, which have a great impact on the fruit quality and yield. However, no studies on the genetic inheritance and quantitative trait locus mapping of heat tolerance in cucumber at the adult stage have been reported yet. In this study, a set of 86 recombinant inbred lines (RILs) derived from “99281” (heat-tolerant) and “931” (heat-sensitive) were used to identify the heat tolerance QTL in summer 2018, 2019, and 2020. Eight-week-old plants were exposed to a natural high temperature environment in the field, and the heat injury index was used to indicate the heat tolerance performance. Genetic analysis showed that the heat tolerance of adult cucumber is quantitatively inherited. One QTL named qHT1.1 on chromosome 1 was identified. It was delimited by Indel 3-3 and Indel 1-15 and explained 59.6%, 58.1%, and 40.1% of the phenotypic variation in 2018, 2019, and 2020, respectively. The efficiency of marker HT-1, which is closely linked to the locus, was tested using 62 cucumber germplasm accessions and was found to have an accuracy of 97.8% in heat sensitive plants. The qHT1.1 was delimited to a 694.5-kb region, containing 98 genes, nine of which may be involved in heat tolerance. Further sequence analysis showed that there are three single-base substitutions within the coding sequences of Csa1G004990. Gene expression analyses suggested that the expression of Csa1G004990 was significantly higher in “99281” than “931” at 14d, 35d, 42d, and 49d after transplanting. This study provides practically useful markers for heat tolerance breeding in cucumber and provides a basis for further identifying heat tolerant genes.

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Section: Qtl Mapping Of Heat Tolerancementioning

confidence: 99%

QTL Mapping of Heat Tolerance in Cucumber (Cucumis sativus L.) at Adult Stage

Liu

Dong

Wei

et al. 2021

Plants

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“…However, the names of the QTL are confusing in the literature. For convenience, following recommendations for QTL naming by Pan et al (2020) and Wang et al (2020), here we developed a QTL nomenclature for naming QTL for seed-related traits, which are presented in Table 1. In brief, SL, SWD, ST, and 100SWT stood for the seed length, seed width, seed thickness and 100-seed weight, respectively.…”

Section: Qtl For Seed Size (Ss) Variation In Major Cucurbit Cropsmentioning

confidence: 99%

Quantitative Trait Loci for Seed Size Variation in Cucurbits – A Review

et al. 2020

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Cucurbits (Cucurbitaceae family) include many economically important fruit vegetable crops such as watermelon, pumpkin/squash, cucumber, and melon. Seed size (SS) is an important trait in cucurbits breeding, which is controlled by quantitative trait loci (QTL). Recent advances have deciphered several signaling pathways underlying seed size variation in model plants such as Arabidopsis and rice, but little is known on the genetic basis of SS variation in cucurbits. Here we conducted literature review on seed size QTL identified in watermelon, pumpkin/squash, cucumber and melon, and inferred 14, 9 and 13 consensus SS QTL based on their physical positions in respective draft genomes. Among them, four from watermelon (ClSS2.2, ClSS6.1, ClSS6.2, and ClSS8.2), two from cucumber (CsSS4.1 and CsSS5.1), and one from melon (CmSS11.1) were majoreffect, stable QTL for seed size and weight. Whole genome sequence alignment revealed that these major-effect QTL were located in syntenic regions across different genomes suggesting possible structural and functional conservation of some important genes for seed size control in cucurbit crops. Annotation of genes in the four watermelon consensus SS QTL regions identified genes that are known to play important roles in seed size control including members of the zinc finger protein and the E3 ubiquitinprotein ligase families. The present work highlights the utility of comparative analysis in understanding the genetic basis of seed size variation, which may help future mapping and cloning of seed size QTL in cucurbits.

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“…Downy mildew was also devastating in cucumber. Many researches on downy mildew in cucumber have been reported [10][11][12]. Zhang et al (2013) constructed the F 2 and F 2:3 population based on the cross of inbred line K8 and K18 and identi ed 5 QTLs (dm1.1, dm5.1, dm5.2, dm5.3 and dm6.1) associated with DM on the Chr1, Chr5 and Chr6, respectively.…”

Section: Downy Mildew (Dm) Is Caused By the Obligate Biotrophic Oomycmentioning

confidence: 99%

Identification of novel loci and candidate genes for cucumber downy mildew resistance using GWAS

Liu

et al. 2020

Preprint

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Background Downy mildew (DM) is one of the most serious diseases in cucumber and brings the loss of yield and profit. Multiple QTLs for DM resistance have been detected, however, no loci related to resistance was reported using genome-wide association analysis (GWAS). In this study, the core germplasm (CG) of cucumber lines that had been constructed and resequenced were used to identify DM resistance Loci using GWAS technology. Results Thirteen loci (dmG1.1, dmG1.2, dmG2.1, dmG2.2, dmG3.1, dmG4.1, dmG4.2, dmG5.1, dmG5.2, dmG6.1, dmG6.2, dmG7.1 and dmG7.2) associated with DM resistance were detected on all the seven chromosomes. Among these loci, dmG2.1 and dmG7.1 were novel loci compared with previous studies. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlations, Csa1G575030 could be the most likely candidate gene of dmG1.2; Csa2G059820 and Csa2G060360 could be the candidate gene of dmG2.1. A WRKY transcription factor Csa5G606470 could be the candidate gene of dmG5.2. Csa7G004020 could be the candidate gene of dmG7.1. Conclusions These results identify five candidate genes for four loci related to DM resistance in cucumber which provide theoretical basis for gene cloning and genetic breeding of DM resistance in cucumber.

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Molecularly tagged genes and quantitative trait loci in cucumber with recommendations for QTL nomenclature

Cited by 82 publications

References 105 publications

QTL Mapping of Heat Tolerance in Cucumber (Cucumis sativus L.) at Adult Stage

QTL Mapping of Heat Tolerance in Cucumber (Cucumis sativus L.) at Adult Stage

Quantitative Trait Loci for Seed Size Variation in Cucurbits – A Review

Identification of novel loci and candidate genes for cucumber downy mildew resistance using GWAS

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