A combined BSA-Seq and linkage mapping approach identifies genomic regions associated with Phytophthora root and crown rot resistance in squash

Genomics assisted mapping of earliness in pea (Pisum sativum L.)

BACKGROUND

Garden pea (Pisum sativum L.), is a temperate crop belonging to the Leguminosae family. Early maturing pea varieties complete their growth cycle in ∼80-90 days and fits very well within the crop rotation of rice, wheat, and maize, thereby providing an extra source of income to the farmers. Identification of genes associated with the earliness is very important for developing early maturing pea varieties.

METHODS AND RESULTS

In the present study we investigated the genetics of earliness and identified the putative genomic regions associated with the earliness in F2 population derived from a cross between early-maturing (Matar Ageta-10) and late-maturing (Punjab-89) pea varieties using BSA-Seq approach. Genetic analysis revealed that earliness follows a monogenic recessive inheritance pattern. Two extreme phenotypic pools were constructed by identifying ten extreme early and ten extreme late plants from the F2 population, and QTL-seq analysis was performed to obtain major genomic region of 6.5 Mb located at 418.46 Mb to 424.97 Mb on chromosome 7 and has been designated as PsE7. Further, a total of 907 SNPs were identified within this 6.5 Mb genomic region of which seven SNPs were validated through KASP markers. Among these, one marker namely PS423028253 showed association with the earliness trait at distance of 1.7 cM.

CONCLUSION

This novel genomic region along with KASP marker (PS423028253) identified in this study could be used for marker-assisted selection in pea breeding programs and will aid in the identification of the candidate genes in future studies.

The Identification of a Single-Base Mutation in the Maize Dwarf 1 Gene Responsible for Reduced Plant Height in the Mutant 16N125

Maize (Zea mays L.) is a globally vital crop for food, feed, and biofuel production, with plant height (PH) being a key agronomic trait that significantly influences yield, lodging resistance, and stress tolerance. This study identified a single-base mutation in the D1 (Dwarf 1) gene responsible for the dwarf phenotype in the maize mutant 16N125. Through genetic analysis and fine mapping, the candidate region was localized to chromosome 3, narrowing it down to an interval containing three genes. Sequencing revealed a non-synonymous mutation in D1, which encodes a gibberellin 3-beta-dioxygenase, leading to amino acid substitutions at positions 61 and 123. Genetic analysis of F2 populations confirmed that the mutation at position 61 was responsible for the dwarf trait. Furthermore, the mutation was detected in several Chinese inbred lines, indicating its potential role in dwarfing under specific conditions. These findings provide critical insights into the genetic mechanisms regulating maize plant height, offering valuable information for breeding programs focused on improving crop architecture and yield to address the challenges of global food security and climate change.

Novel Allelic Mutations in Dw3 Gene That Affect the Height of Sorghum Plants

Breeding for dwarfing traits in sorghum is crucial. However, only three genes (Dw1-Dw3) that control plant height have been mapped. In this study, 634 sorghum cultivars were collected to investigate plant height and genotypes. Four were genotyped Dw1DW2Dw3 (wild type) but with different plant heights, and they were selected to construct two populations and map new dwarf genes. Bulked segregant analysis with whole-genome resequencing of the two populations identified the candidate gene in one same genomic region-on chromosome 7. Then, it was narrowed down to a region containing nine genes. Amino acid and DNA sequence analysis of the parent and offspring plants revealed that two novel allelic mutations in the Dw3 gene play a role in reducing the plant height-8R262 or 8R417, including 1 bp substitution and 2 bp deletions. Furthermore, we sequenced 19 cultivars that primarily exhibited a "one-dwarf" hybrid or wild-type and presumed another allelic mutation via the amino acid alignment of 8R019, 8R100, and 8R402, which was another one-base substitution. These results indicate that multiple types of allelic mutations in the Dw3 gene should be considered when identified or applied.

Identification of Dwarfing Candidate Genes in Brassica napus L. LSW2018 through BSA-Seq and Genetic Mapping

Plant height, as a crucial component of plant architecture, exerts a significant influence on rapeseed (Brassica napus L.) lodging resistance, photosynthetic efficiency, yield, and mechanized harvest level. A previous study identified dwarf rapeseed LSW2018. In this study, LSW2018 (dwarf parent (PD)) was crossed with 389 (high parent (PH)) to establish the F2 population, and 30 extremely dwarf (bulk-D) and high (bulk-H) plants in the F2 population were respectively selected to construct two bulked DNA pools. Whole-genome sequencing and variation analysis (BSA-seq) were performed on these four DNA pools (PD, PH, bulk-D, and bulk-H). The BSA-seq results revealed that the genomic region responsible for the dwarf trait spanned from 19.30 to 22.19 Mb on chromosome A03, with a length of 2.89 Mb. After fine mapping with simple sequence repeat (SSR) markers, the gene was narrowed to a 0.71 Mb interval. Within this region, a total of 113 genes were identified, 42 of which contained large-effect variants. According to reference genome annotation and qRT-PCR analysis, there are 17 differentially expressed genes in this region between high and dwarf individuals. This study preliminarily reveals the genetic basis of LSW2018 dwarfing and provides a theoretical foundation for the molecular marker-assisted breeding of dwarf rapeseed.

A multifaceted crosstalk between brassinosteroid and gibberellin regulates the resistance of cucumber to Phytophthora melonis

Cucumber plants are highly susceptible to the hemibiotroph oomycete Phytophthora melonis. However, the mechanism of resistance to cucumber blight remains poorly understood. Here, we demonstrated that cucumber plants with impairment in the biosynthesis of brassinosteroids (BRs) or gibberellins (GAs) were more susceptible to P. melonis. By contrast, increasing levels of endogenous BRs or exogenously application of 24-epibrassinolide enhanced the resistance of cucumber plants against P. melonis. Furthermore, we found that both knockout and overexpression of the BR biosynthesis gene CYP85A1 reduced the endogenous GA3 content compared with that of wild-type plants under the condition of inoculation with P. melonis, and the enhancement of disease resistance conferred by BR was inhibited in plants with silencing of the GA biosynthetic gene GA20ox1 or KAO. Together, these findings suggest that GA homeostasis is an essential factor mediating BRs-induced disease resistance. Moreover, BZR6, a key regulator of BR signaling, was found to physically interact with GA20ox1, thereby suppressing its transcription. Silencing of BZR6 promoted endogenous GA biosynthesis and compromised GA-mediated resistance. These findings reveal multifaceted crosstalk between BR and GA in response to pathogen infection, which can provide a new approach for genetically controlling P. melonis damage in cucumber production.

Identification of Clubroot (Plasmodiophora brassicae) Resistance Loci in Chinese Cabbage (Brassica rapa ssp. pekinensis) with Recessive Character

The soil-borne pathogen Plasmodiophora brassicae is the causal agent of clubroot, a major disease in Chinese cabbage (Brassica rapa ssp. pekinensis). The host's resistance genes often confer immunity to only specific pathotypes and may be rapidly overcome. Identification of novel clubroot resistance (CR) from germplasm sources is necessary. In this study, Bap246 was tested by being crossed with different highly susceptible B. rapa materials and showed recessive resistance to clubroot. An F2 population derived from Bap246 × Bac1344 was used to locate the resistance Quantitative Trait Loci (QTL) by Bulk Segregant Analysis Sequencing (BSA-Seq) and QTL mapping methods. Two QTL on chromosomes A01 (4.67-6.06 Mb) and A08 (10.42-11.43 Mb) were found and named Cr4Ba1.1 and Cr4Ba8.1, respectively. Fifteen and eleven SNP/InDel markers were used to narrow the target regions in the larger F2 population to 4.67-5.17 Mb (A01) and 10.70-10.84 Mb (A08), with 85 and 19 candidate genes, respectively. The phenotypic variation explained (PVE) of the two QTL were 30.97% and 8.65%, respectively. Combined with gene annotation, mutation site analysis, and real-time quantitative polymerase chain reaction (qRT-PCR) analysis, one candidate gene in A08 was identified, namely Bra020861. And an insertion and deletion (InDel) marker (co-segregated) named Crr1-196 was developed based on the gene sequence. Bra013275, Bra013299, Bra013336, Bra013339, Bra013341, and Bra013357 in A01 were the candidate genes that may confer clubroot resistance in Chinese cabbage. The resistance resource and the developed marker will be helpful in Brassica breeding programs.

Conjunctive Analysis of BSA-Seq and SSR Markers Unveil the Candidate Genes for Resistance to Rice False Smut

Rice false smut (RFS) caused by the fungus Ustilaginoidea virens (Cook) leads to serious yield losses in rice. Identification of the gene or quantitative trait loci (QTLs) is crucial to resistance breeding and mitigation of RFS damage. In this study, we crossed a resistant variety, IR77298-14-1-2::IRGC117374-1, with a susceptible indica cultivar, 9311, and evaluated recombinant inbred lines in a greenhouse. The genetic analysis showed that the RFS resistance of IR77298-14-1-2::IRGC117374-1 was controlled by multiple recessive loci. We identified a novel QTL, qRFS12.01, for RFS resistance in IR77298-14-1-2::IRGC117374-1 by combining bulked segregant analysis with whole genome resequencing (BSA-seq) and simple sequence repeat (SSR) marker mapping approaches. The phenotypic effect of qRFS12.01 on RFS resistance reached 28.74%, suggesting that SSR markers linked to qRFS12.01 are valuable for marker-assisted breeding of RFS resistance in rice. The prediction of putative candidate genes within qRFS12.01 revealed five disease resistance proteins containing NB-ARC domains. In conclusion, our findings provide a new rice chromosome region carrying genes/QTLs for resistance to RFS.

Phytophthora capsici: Recent Progress on Fundamental Biology and Disease Management 100 Years After Its Description

Phytophthora capsici is a destructive oomycete pathogen of vegetable, ornamental, and tropical crops. First described by L.H. Leonian in 1922 as a pathogen of pepper in New Mexico, USA, P. capsici is now widespread in temperate and tropical countries alike. Phytophthora capsici is notorious for its capability to evade disease management strategies. High genetic diversity allows P. capsici populations to overcome fungicides and host resistance, the formation of oospores results in long-term persistence in soils, zoospore differentiation in the presence of water increases epidemic potential, and a broad host range maximizes economic losses and limits the effectiveness of crop rotation. The severity of disease caused by P. capsici and management challenges have led to numerous research efforts in the past 100 years. Here, we discuss recent findings regarding the biology, genetic diversity, disease management, fungicide resistance, host resistance, genomics, and effector biology of P. capsici.

Identification of a Major-Effect Quantitative Trait Loci Associated with Begomovirus Resistance in Cucurbita moschata

Begomoviruses, viz. squash leaf curl China virus and tomato leaf curl New Delhi virus causative diseases are major concerns of quantitative and qualitative losses in pumpkin (Cucurbita moschata) worldwide. Punjab Agricultural University (PAU) in India has identified a resistant source (PVR-1343) against mixed infection (MI-Sq/To) of these begomoviruses. Introgression of resistance in diverse genetic backgrounds requires the identification of quantitative trait loci (QTLs) associated with MI-Sq/To resistance. Phenotyping of 229 F_2:3 progenies derived from the PVR-1343 × P-135 cross revealed digenic recessive inheritance against MI-Sq/To resistance in PVR-1343. To identify the genomic region, resistant and susceptible bulks were subjected to whole-genome resequencing along with their parents. The whole-genome resequence analysis of parents and bulks using QTLseq/QTLseqr approaches identified an overlapping 1.52 Mb region on chromosome 7 (qMI-Sq/To7.1), while chromosomal region spanning 0.87 Mb on chromosome17 (qMI-Sq/To17.1) was additionally identified by QTLseqr. However, the highest peak value on chromosome 7 with three algorithms {G', ∆(SNP-index) and -log₁₀ (P value)} highlighted the major contribution of qMI-Sq/To7.1 in MI-Sq/To resistance. Nine polymorphic SNPs identified within the highly significant qMI-Sq/To7.1 region were converted into KASP markers. KASP genotyping of F₂ individuals narrowed down the qMI-Sq/To7.1 interval to 103 kb region flanked by two markers, Cmo3914729 and Cmo4018182, which contained 16 annotated genes and accounted for 59.84% of phenotypic variation. The Cmo4018182 KASP marker accurately predicted disease reaction in 91% of diverse Cucurbita genotypes and showed nonsynonym substitutions in the coding region of putative candidate SYNTAXIN-121 gene. These findings pave the way for marker-assisted breeding and elucidating the underlying mechanism of begomovirus resistance in C. moschata.

Characterization of the USDA Cucurbita pepo, C. moschata, and C. maxima germplasm collections

The Cucurbita genus is home to a number of economically and culturally important species. We present the analysis of genotype data generated through genotyping-by-sequencing of the USDA germplasm collections of Cucurbita pepo, C. moschata, and C. maxima. These collections include a mixture of wild, landrace, and cultivated specimens from all over the world. Roughly 1,500 - 32,000 high-quality single nucleotide polymorphisms (SNPs) were called in each of the collections, which ranged in size from 314 to 829 accessions. Genomic analyses were conducted to characterize the diversity in each of the species. Analysis revealed extensive structure corresponding to a combination of geographical origin and morphotype/market class. Genome-wide associate studies (GWAS) were conducted using both historical and contemporary data. Signals were observed for several traits, but the strongest was for the bush (Bu) gene in C. pepo. Analysis of genomic heritability, together with population structure and GWAS results, was used to demonstrate a close alignment of seed size in C. pepo, maturity in C. moschata, and plant habit in C. maxima with genetic subgroups. These data represent a large, valuable collection of sequenced Cucurbita that can be used to direct the maintenance of genetic diversity, for developing breeding resources, and to help prioritize whole-genome re-sequencing.

Identification and characterization analysis of candidate genes controlling mushroom leaf development in Chinese kale by BSA-seq

Mushroom leaves (MLs) are malformed leaves that develop from the leaf veins in some of Chinese kale genotypes. To study the genetic model and molecular mechanism of ML development in Chinese kale, the F2 segregation population was constructed by two inbred lines, genotype Boc52 with ML and genotype Boc55 with normal leaves (NL). In the present study, we have identified for the first time that the development of mushroom leaves may be affected by the change of adaxial-abaxial polarity of leaves. Examination of the phenotypes of F1 and F2 segregation populations suggested that ML development is controlled by two dominant major genes inherited independently. BSA-seq analysis showed that a major quantitative trait locus (QTL) qML4.1 that controls ML development is located within 7.4 Mb on chromosome kC4. The candidate region was further narrowed to 255 kb by linkage analysis combined with insertion/deletion (InDel) markers, and 37 genes were predicted in this region. According to the expression and annotation analysis, a B3 domain-containing transcription factor NGA1-like gene, BocNGA1, was identified as a key candidate gene for controlling ML development in Chinese kale. Fifteen single nucleotide polymorphisms (SNPs) were found in coding sequences and 21 SNPs and 3 InDels found in the promoter sequences of BocNGA1 from the genotype Boc52 with ML. The expression levels of BocNGA1 in ML genotypes are significantly lower than in the NL genotypes, which suggests that BocNGA1 may act as a negative regulator for ML genesis in Chinese kale. This study provides a new foundation for Chinese kale breeding and for the study of the molecular mechanism of plant leaf differentiation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01364-6.

Quantitative trait locus mapping and identification of candidate genes for resistance to Verticillium wilt in four recombinant inbred line populations of Gossypium hirsutum

Improving resistance to Verticillium wilt is of great significance for achieving high and stable yields of Upland cotton (Gossypium hirsutum). To deeply understand the genetic basis of cotton resistance to Verticillium wilt, Verticillium wilt-resistant Upland Lumianyan 28 and four Verticillium wilt-susceptible Acala cotton cultivars were used to create four recombinant inbred line (RIL) populations of 469 families through nested hybridization. Phenotypic data collected in five stressful environments were used to select resistant and sensitive lines and create a mixed pool of extreme phenotypes for BSA-seq. A total of 8 QTLs associated with Verticillium wilt resistance were identified on 4 chromosomes, of which qVW-A12-5 was detected simultaneously in the RIL populations and in one of the RIL populations and was identified for the first time. According to the sequence comparison and transcriptome analysis of candidate genes in the QTL interval between parents and pools, 4 genes were identified in the qVW-A12-5 interval. qRT-PCR of parental and phenotypically extreme lines revealed that Gh_CPR30 was induced by and may be a candidate gene for resistance to Verticillium wilt in G. hirsutum. Furthermore, VIGS technology revealed that the disease severity index (DSI) of the Gh_CPR30-silenced plants was significantly higher than that of the control. These results indicate that the Gh_CPR30 gene plays an important role in the resistance of G. hirsutum to Verticillium wilt, and the study provides a molecular basis for analyzing the molecular mechanism underlying G. hirsutum resistance to Verticillium wilt.

Phenotypic analysis of Longya-10 × pale flax hybrid progeny and identification of candidate genes regulating prostrate/erect growth in flax plants

Flax is a dual-purpose crop that is important for oil and fiber production. The growth habit is one of the crucial targets of selection during flax domestication. Wild hybridization between cultivated flax and wild flax can produce superior germplasms for flax breeding and facilitate the study of the genetic mechanism underlying agronomically important traits. In this study, we used pale flax, Linum grandiflorum, and L. perenne to pollinate Longya-10. Only pale flax interspecific hybrids were obtained, and the trait analysis of the F₁ and F₂ generations showed that the traits analyzed in this study exhibited disparate genetic characteristics. In the F₁ generation, only one trait, i.e., the number of capsules per plant (140) showed significant heterosis, while the characteristics of other traits were closely associated with those of the parents or a decline in hybrid phenotypes. The traits of the F₂ generation were widely separated, and the variation coefficient ranged from 9.96% to 146.15%. The quantitative trait locus underlying growth habit was preliminarily found to be situated on chromosome 2 through Bulked-segregant analysis sequencing. Then linkage mapping analysis was performed to fine-map GH2.1 to a 23.5-kb interval containing 4 genes. Among them, L.us.o.m.scaffold22.109 and L.us.o.m.scaffold22.112 contained nonsynonymous SNPs with Δindex=1. Combined with the qRT-PCR results, the two genes might be possible candidate genes for GH2.1. This study will contribute to the development of important germplasms for flax breeding, which would facilitate the elucidation of the genetic mechanisms regulating the growth habit and development of an ideal architecture for the flax plant.

A Genomic BSAseq Approach for the Characterization of QTLs Underlying Resistance to Fusarium oxysporum in Eggplant

Eggplant (Solanum melongena L.), similar to many other crops, suffers from soil-borne diseases, including Fusarium oxysporum f. sp. melongenae (Fom), causing wilting and heavy yield loss. To date, the genetic factors underlying plant responses to Fom are not well known. We previously developed a Recombinant Inbred Lines (RILs) population using as a female parent the fully resistant line '305E40' and as a male parent the partially resistant line '67/3'. The fully resistant trait to Fom was introgressed from the allied species S. aethiopicum. In this work, the RIL population was assessed for the responses to Fom and by using a genomic mapping approach, two major QTLs on chromosomes CH02 and CH11 were identified, associated with the full and partial resistance trait to Fom, respectively. A targeted BSAseq procedure in which Illumina reads bulks of RILs grouped according to their resistance score was aligned to the appropriate reference genomes highlighted differentially enriched regions between resistant/susceptible progeny in the genomic regions underlying both QTLs. The characterization of such regions allowed us to identify the most reliable candidate genes for the two resistance traits. With the aim of revealing exclusive species-specific contigs and scaffolds inherited from the allied species and thus associated with the full resistance trait, a draft de-novo assembly of available Illumina sequences of the '305E40' parent was developed to better resolve the non-recombining genomic region on its CH02 carrying the introgressed Fom resistance locus from S. aethiopicum.

Harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding

Most plant traits are governed by polygenes including both major and minor genes. Linkage mapping and positional cloning have contributed greatly to mapping genomic loci controlling important traits in crop species. However, they are low-throughput, time-consuming, and have low resolution due to which their efficiency in crop breeding is reduced. In this regard, the bulk segregant analysis sequencing (BSA-seq) and its related approaches, viz., quantitative trait locus (QTL)-seq, bulk segregant RNA-Seq (BSR)-seq, and MutMap, have emerged as efficient methods to identify the genomic loci/QTLs controlling specific traits at high resolution, accuracy, reduced time span, and in a high-throughput manner. These approaches combine BSA with next-generation sequencing (NGS) and enable the rapid identification of genetic loci for qualitative and quantitative assessments. Many previous studies have shown the successful identification of the genetic loci for different plant traits using BSA-seq and its related approaches, as discussed in the text with details. However, the efficiency and accuracy of the BSA-seq depend upon factors like sequencing depth and coverage, which enhance the sequencing cost. Recently, the rapid reduction in the cost of NGS together with the expected cost reduction of third-generation sequencing in the future has further increased the accuracy and commercial applicability of these approaches in crop improvement programs. This review article provides an overview of BSA-seq and its related approaches in crop breeding together with their merits and challenges in trait mapping.

Evaluation of nine statistics to identify QTLs in bulk segregant analysis using next generation sequencing approaches

Background

Bulk segregant analysis (BSA) combined with next generation sequencing is a powerful tool to identify quantitative trait loci (QTL). The impact of the size of the study population and the percentage of extreme genotypes analysed have already been assessed. But a good comparison of statistical approaches designed to identify QTL regions using next generation sequencing (NGS) technologies for BSA is still lacking.

Results

We developed an R code to simulate QTLs in bulks of F2 contrasted lines. We simulated a range of recombination rates based on estimations using different crop species. The simulations were used to benchmark the ability of statistical methods identify the exact location of true QTLs. A single QTL led to a shift in allele frequency across a large fraction of the chromosome for plant species with low recombination rate. The smoothed version of all statistics performed best notably the smoothed Euclidean distance-based statistics was always found to be more accurate in identifying the location of QTLs. We propose a simulation approach to build confidence interval statistics for the detection of QTLs.

Conclusion

We highlight the statistical methods best suited for BSA studies using NGS technologies in crops even when recombination rate is low. We also provide simulation codes to build confidence intervals and to assess the impact of recombination for application to other studies. This computational study will help select NGS-based BSA statistics that are useful to the broad scientific community.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08718-y.

Whole Genome Re-sequencing and Bulk Segregant Analysis Reveals Chromosomal Location for Papaya Ringspot Virus W Resistance in Squash

Squash (Cucurbita moschata) is among the most important cucurbit crops grown worldwide. Plant pathogen, Papaya ringspot virus W (PRSV-W) causes significant yield loss in commercial squash production globally. The development of virus-resistant cultivars can complement integrated disease management and mitigate losses due to viral infections. However, the genetic loci and molecular markers linked to PRSV-W resistance that could facilitate marker-assisted selection (MAS) for accelerated cultivar development are unknown. In this study, quantitative trait loci (QTL), molecular markers, and candidate genes associated with PRSV-W resistance in squash were identified in an F₂ population (n = 118) derived from a cross between Nigerian Local accession (resistant) and Butterbush cultivar (susceptible). Whole genome re-sequencing-based bulked segregant analysis (QTLseq method; n = 10 for each bulk) and non-parametric interval mapping were used to identify a major QTL associated with PRSV-W resistance on chromosome 9 (QtlPRSV-C09) (p < 0.05) of C. moschata. QtlPRSV-C09 extended from 785,532 to 5,093,314 bp and harbored 12,245 SNPs among which 94 were high-effect variants. To validate QtlPRSV-C09, 13 SNP markers were assayed as Kompetitive allele-specific PCR (KASP) markers in the F₂ population and tested for the association with PRSV-W resistance. Among these, two KASP markers (Ch09_2080834 and Ch09_5023865-1) showed significant association with PRSV-W resistance (p < 0.05). The two SNPs were located within exons of putative disease-resistant genes encoding the clathrin assembly family and actin cytoskeleton-regulatory complex proteins, which are implicated in disease resistance across plant species. The findings of this study will facilitate MAS for PRSV-W resistance in squash and allow further understanding of the functional mechanisms underlying potyvirus resistance in Cucurbita species.

Genomic Position and Markers Associated with the Hull-Less Seed Trait in Pumpkin

Pumpkin (Cucurbita pepo) seeds are nutritious and valued as a source of vegetable oil, protein, healthy fatty acids, and minerals. Pumpkin seeds that are naturally devoid of the seedcoat (hull-less) are preferred by the industry as they eliminate the need for de-hulling prior to use. A single recessive gene, designated as n or h, controls the hull-less seed trait in pumpkin. Visual selection for the trait is easy, however, it is resource intensive when applied to large breeding populations. High throughput genotyping assays can aid in the identification of suitable individuals in segregating populations through marker-assisted selection. In the current study, the QTL-seq approach was used to identify genetic loci, SNP markers and candidate genes associated with the hull-less trait in a segregating F2 population (n = 143) derived from a cross between Kakai (hull-less) × Table Gold Acorn (hulled). The segregation of the hull-less trait in the F2 population fit a 3:1 ratio (p < 0.05). QTL-seq analysis detected a single QTL on chromosome 12 (Qtlhull-less-C12) which was significantly associated with the hull-less trait in C. pepo. Twenty-eight SNPs were genotyped in the population, two among which (Ch12_3412046 and Ch12_3417142) were significantly associated (p < 0.05) with the hull-less trait in cultivars and accessions of diverse genetic background. Several candidate genes fall within the Qtlhull-less-C12 interval, among them is the No Apical meristem (NAC) domain-containing protein and a Fiber Protein fb11 gene involved in lignin accumulation and cell wall deposition across plant species, respectively. The findings of this study will facilitate the marker-assisted selection for the hull-less seed trait in pumpkin and further our understanding of the functional mechanisms underlying the trait across cucurbit crops.

Tolerance Screening for Phytophthora capsici and Fusarium solani f. sp. cucurbitae in Cucurbita spp. and Gene Expression Responses in Mutant Families

Cucurbita species can be affected by soil-borne pathogens, such as Phytopthora capsici and Fusarium solani f. sp. cucurbitae (Fsc). Diverse commercial and conserved lines of Cucurbita spp. were tested. C. pepo subsp. pepo genotypes showed the highest susceptibility to both pathogens. The tolerance to P. capsici and Fsc was then screened in a zucchini mutant population. Two M3 mutant lines (Cp107 and Cp116) with a high occurrence of tolerant individuals to Phytophthora capsici were obtained from a screening of 160 M2 mutant lines. The M3 lines presented higher tolerance than the background MUCU-16. Furthermore, in the inoculated samples, both mutants overexpressed CpDEF and expressed more CpPAL and CpChiIV than the susceptible control. It has been previously shown that this expression pattern could be associated with tolerance in the P. capsici - Cucurbita spp. pathosystem. The M3 lines obtained could be applied in breeding programs, as they are likely to be compatible with the highly susceptible C. pepo subsp. pepo genotype.

Broad Resistance to Post-Harvest Fruit Rot in USVL Watermelon Germplasm Lines to Isolates of Phytophthora capsici Across the United States

Watermelon is an important cucurbit vegetable crop grown in most of the United States. Phytophthora fruit rot of watermelon caused by Phytophthora capsici has been a major factor, limiting production for the past 15 years in the southeastern United States. The U.S. Department of Agriculture, Agricultural Research Service released five Phytophthora fruit rot-resistant germplasm lines for use in breeding programs. These lines were developed by phenotyping using a local isolate of P. capsici from South Carolina. The present study was undertaken to determine if these resistant lines had broad resistance to diverse P. capsici isolates collected from different states and crops. Five resistant germplasm lines (USVL020-PFR, USVL203-PFR, USVL782-PFR, USVL489-PFR, and USVL531-MDR) and two susceptible cultivars, Sugar Baby and Mickey Lee, used as checks were grown in a field in 2014 and 2015 to produce fruit for evaluation. Mature fruit were harvested and placed in a walk-in growth chamber and inoculated with 20 different P. capsici isolates. The chamber was maintained at 26 ± 2°C and high relative humidity (>95%) using a humidifier. All five resistant germplasm lines were significantly more resistant than the two susceptible checks to all 20 P. capsici isolates. Among the five resistant germplasm lines, USVL020-PFR, USVL782-PFR, and USVL531-MDR had broad resistance. Some P. capsici isolates induced minor lesions and rot on USVL489-PFR compared with the other resistant lines. Variation in virulence and genetic diversity among the 20 P. capsici isolates was also observed. The five watermelon germplasm lines will be useful for developing commercial watermelon cultivars with broad resistance to P. capsici.

A Novel QTL for Resistance to Phytophthora Crown Rot in Squash

Phytophthora capsici Leonian causes significant yield losses in commercial squash (Cucurbita pepo) production worldwide. The deployment of resistant cultivars can complement integrated management practices for P. capsici, but resistant cultivars are currently unavailable for growers. Moderate resistance to Phytophthora crown rot in a selection of accession PI 181761 (C. pepo) (designated line #181761-36P) is controlled by three dominant genes (R4, R5 and R6). Introgression of these loci into elite germplasm through marker-assisted selection (MAS) can accelerate the release of new C. pepo cultivars resistant to crown rot, but these tools are currently unavailable. Here we describe the identification of a quantitative trait locus (QTL), molecular markers and candidate genes associated with crown rot resistance in #181761-36P. Five hundred and twenty-three SNP markers were genotyped in an F₂ (n = 83) population derived from a cross between #181761-36P (R) and Table Queen (S) using targeted genotyping by sequencing. A linkage map (2068.96 cM) consisting of twenty-one linkage groups and an average density of 8.1 markers/cM was developed for the F₂ population. The F₂:₃ families were phenotyped in the greenhouse with a virulent strain of P. capsica, using the spore-spray method. A single QTL (QtlPC-C13) was consistently detected on LG 13 (chromosome 13) across three experiments and explained 17.92-21.47% of phenotypic variation observed in the population. Nine candidate disease resistance gene homologs were found within the confidence interval of QtlPC-C13. Single nucleotide polymorphism (SNP) markers within these genes were converted into Kompetitive Allele Specific PCR (KASP) assays and tested for association with resistance in the F₂ population. One SNP marker (C002686) was significantly associated with resistance to crown rot in the F₂ population (p < 0.05). This marker is a potential target for MAS for crown rot resistance in C. pepo.

Genetic Mapping and Identification of the Candidate Gene for White Seed Coat in Cucurbita maxima

Seed coat color is an important agronomic trait of edible seed pumpkin in Cucurbita maxima. In this study, the development pattern of seed coat was detected in yellow and white seed coat accessions Wuminglv and Agol. Genetic analysis suggested that a single recessive gene white seed coat (wsc) is involved in seed coat color regulation in Cucurbita maxima. An F₂ segregating population including 2798 plants was used for fine mapping and a candidate region containing nine genes was identified. Analysis of 54 inbred accessions revealed four main Insertion/Deletion sites in the promoter of CmaCh15G005270 encoding an MYB transcription factor were co-segregated with the phenotype of seed coat color. RNA-seq analysis and qRT-PCR revealed that some genes involved in phenylpropanoid/flavonoid metabolism pathway displayed remarkable distinction in Wuminglv and Agol during the seed coat development. The flanking InDel marker S1548 was developed to predict the seed coat color in the MAS breeding with an accuracy of 100%. The results may provide valuable information for further studies in seed coat color formation and structure development in Cucurbitaceae crops and help the molecular breeding of Cucurbita maxima.