Genetic Linkage Map Construction and QTL Analysis of Two Interspecific Reproductive Isolation Traits in Sponge Gourd

Ren

Molecular Ecology Resources

et al. 2020

Sponge gourd (Luffa cylindrica (L.) Roem.) or luffa is a diploid herbaceous plant with 26 chromosomes (2n = 26) and belongs to the family Cucurbitaceae. To address the limited knowledge of the genome of Luffa species, the chromosome‐level genome of L. cylindrica was assembled and analysed using PacBio long reads and Hi‐C data. We combined Hi‐C data with a draft genome assembly to generate chromosome‐length scaffolds. Thirteen scaffolds corresponding to the 13 chromosomes were assembled from 1,156 contigs to a final size of 669 Mb with a contig N50 size of 5 Mb and a scaffold N50 size of 53 Mb. After removing redundant sequences, 416.31 Mb (62.18% of the genome) of repeat sequences was detected. Subsequently, 31,661 protein‐coding genes with an average of 5.69 exons per gene were identified in the L. cylindrica genome using de novo methods, transcriptome data and homologue‐based approaches. In addition, 27,552 protein‐coding genes (87.02%) were annotated in five databases. According to the phylogenetic analysis, L. cylindrica is closely related to Cucurbita and Cucumis species and diverged from their common ancestor ~28.6–67.1 million years ago. Genome collinearity analysis was performed in Cucurbita moschata, Cucumis sativus and L. cylindrica, and it demonstrated a high degree of conserved gene order in these three species. The completeness of the genome will provide high‐quality genomic knowledge on breeding and reveal genetic variation in L. cylindrica.

Section: Introductionmentioning

confidence: 99%

Long‐read sequencing and de novo assembly of the Luffa cylindrica (L.) Roem. genome

Ren

Molecular Ecology Resources

et al. 2020

“…Luffa , or sponge gourd, belonging to the Cucurbitaceae family, is a diploid species with 26 chromosomes (2 n = 26) and a cross pollinated crop [ 1 ]. Luffa cylindrica (L.) Roem.…”

Section: Introductionmentioning

confidence: 99%

Genome Survey Sequencing of Luffa Cylindrica L. and Microsatellite High Resolution Melting (SSR-HRM) Analysis for Genetic Relationship of Luffa Genotypes

Yin

et al. 2017

IJMS

Luffa cylindrica (L.) Roem. is an economically important vegetable crop in China. However, the genomic information on this species is currently unknown. In this study, for the first time, a genome survey of L. cylindrica was carried out using next-generation sequencing (NGS) technology. In total, 43.40 Gb sequence data of L. cylindrica, about 54.94× coverage of the estimated genome size of 789.97 Mb, were obtained from HiSeq 2500 sequencing, in which the guanine plus cytosine (GC) content was calculated to be 37.90%. The heterozygosity of genome sequences was only 0.24%. In total, 1,913,731 contigs (>200 bp) with 525 bp N50 length and 1,410,117 scaffolds (>200 bp) with 885.01 Mb total length were obtained. From the initial assembled L. cylindrica genome, 431,234 microsatellites (SSRs) (≥5 repeats) were identified. The motif types of SSR repeats included 62.88% di-nucleotide, 31.03% tri-nucleotide, 4.59% tetra-nucleotide, 0.96% penta-nucleotide and 0.54% hexa-nucleotide. Eighty genomic SSR markers were developed, and 51/80 primers could be used in both “Zheda 23” and “Zheda 83”. Nineteen SSRs were used to investigate the genetic diversity among 32 accessions through SSR-HRM analysis. The unweighted pair group method analysis (UPGMA) dendrogram tree was built by calculating the SSR-HRM raw data. SSR-HRM could be effectively used for genotype relationship analysis of Luffa species.

“…Saturated SNP-based high-density genetic linkage map in Luffa Genetic linkage maps are useful tools for fine mapping and map-based cloning [17,24,25]. Two interspecific genetic maps have previously been constructed in Luffa [10,11]. Cui et al (2015) reported the first sponge gourd genetic linkage map, which was constructed using SRAP markers [10].…”

Section: Discussionmentioning

confidence: 99%

“…Cui et al (2015) [10] and Wu et al (2016) [11] used interspecific Luffa spp. crosses for their genetic maps, whereas we used an intraspecific Luffa cylindrica F 2 mapping population in our study, which avoided the marked segregation distortion of molecular markers in interspecific hybridization populations.…”

Section: Discussionmentioning

confidence: 99%

“…Although this map was the first genetic linkage map of Luffa spp, 24 linkage groups more than 13 chromosomes were construct in Cui's study. Wu et al (2016) constructed a more condensed interspecific genetic map, which consists of 177 EST-SSR markers distributed in 14 linkage groups (LG) with an average of 102.58 cM per LG [11]. Due to interspecific hybridization, there was a marked segregation distortion of molecular markers in this map.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Construction of a High-density Genetic Linkage Map and QTL Analysis of Resistance to Cucumber Mosaic Virus in Luffa cylindrica (L.) Roem. Based on Specific Length Amplified Fragment Sequencing

Lou

Liu

et al. 2019

Preprint

Background: Luffa cylindrica L. is an economically important vegetable crop that is consumed globally. Cucumber mosaic virus (CMV) is an important virus affecting Luffa spp. No specific high-density maps have been constructed owing to a lack of efficient markers. Furthermore, no genes or quantitative trait loci (QTLs) are reportedly responsible for CMV resistance in Luffa spp. The development of next-generation sequencing has enabled discovery of single nucleotide polymorphisms and high-throughput genotyping of large populations. Results: A total of 271.01 Mb pair-end reads were generated. The average sequencing depth was 86.19× in both maternal and parental lines, and 14.57× in each F 2 individual. When filtering low-depth specific locus amplified fragment (SLAF) tags, 100,077 high-quality SLAFs were detected, and 7,405 of them were polymorphic. Finally, 3,701 of the polymorphic markers were selected for genetic map construction, and 13 linkage groups were generated. The map spanned 1,518.56 cM with an average distance of 0.41 cM between adjacent markers. Our results also revealed that CMV resistance was regulated by QTLs. Based on the newly constructed high-density map, two loci located on chromosome 1 (100.072 ~ 100.457 cM) and 4 (42.475 ~ 44.398 cM) were identified to regulate CMV resistance in L. cylindrica . A gag-polypeptide of LTR copia-type retrotransposon was predicted as the candidate gene responsible for CMV resistance in L. cylindrica . Conclusions: A high-density linkage map of L. cylindrica was constructed using SLAF. QTL mapping based on CMV disease phenotypes of F 2 led to the identification of two QTL on chromosome 1 and 4, respectively. Kompetitive allele-specific PCR analysis of 60 F 2 individuals, which gave rise to F 2:3 individuals, was carried out. We found that the QTL on chromosome 1 was associated with CMV resistance. Mapping of CMV QTL combined with the transcriptomic sequence alignment identified a gag-polypeptide of LTR copia-type retrotransposon as the most likely causal gene.