QTL mapping and epistatic interaction analysis of field resistance to sudden death syndrome (<Emphasis Type="Italic">Fusarium virguliforme</Emphasis>) in soybean

Key message

Two interactive quantitative trait loci (QTLs) controlled the field resistance to sudden death syndrome (SDS) in soybean. The interaction between them was confirmed.

Abstract

Sudden death syndrome (SDS), caused by Fusarium virguliforme, is a major disease of soybean [Glycine max (L.) Merr.] in the United States. Breeding for soybean resistance to SDS is the most cost-effective method to manage the disease. The objective of this study was to identify and characterize quantitative trait loci (QTLs) underlying field resistance to SDS in a recombinant inbred line population from the cross GD2422?×?LD01-5907. This population was genotyped with 1786 polymorphic single nucleotide polymorphisms (SNPs) using SoySNP6 K iSelect BeadChip and evaluated for SDS resistance in a naturally infested field. Four SDS resistance QTLs were mapped on Chromosomes 4, 8, 12 and 18. The resistant parent, LD01-5907, contributed the resistance alleles for the QTLs on Chromosomes 8 and 18 (qSDS-8 and qSDS-18), while the other parent, GD2422, provided the resistance alleles for the QTLs on Chromosomes 4 and 12 (qSDS-4 and qSDS-12). The minor QTL on Chromosome 12 (qSDS-12) is novel. The QTL on Chromosomes 8 and 18 (qSDS-8 and qSDS-18) overlapped with two soybean cyst nematode resistance-related loci, Rhg4 and Rhg1, respectively. A significant interaction between qSDS-8 and qSDS-18 was detected by disease incidence. Individual effects together with the interaction effect explained around 70% of the phenotypic variance. The epistatic interaction of qSDS-8 and qSDS-18 was confirmed by the field performance across multiple years. Furthermore, the resistance alleles at qSDS-8 and qSDS-18 were demonstrated to be recessive. The SNP markers linked to these QTLs will be useful for marker-assisted breeding to enhance the SDS resistance.

     

Exploring the quantitative resistance to <Emphasis Type="Italic">Pseudomonas syringae</Emphasis> pv. <Emphasis Type="Italic">phaseolicola</Emphasis> in common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.)

Pseudomonas syringae pv. phaseolicola is an important disease that causes halo blight in common bean. The genetic mechanisms underlying quantitative halo blight resistance are poorly understood in this species, as most disease studies have focused on qualitative resistance. The present work examines the genetic basis of quantitative resistance to the nine halo blight races in different organs (primary and trifoliate leaf, stem and pod) of an Andean recombinant inbred line (RIL) progeny. Using a multi-environment quantitative trait locus (QTL) mapping approach, 76 and 101 main-effect and epistatic QTLs were identified, respectively. Most of the epistatic interactions detected were due to loci without detectable QTL additive main effects. Main and epistatic QTLs detected were mainly consistent across the environment conditions. The homologous genomic regions corresponding to 26 of the 76 main-effect detected QTLs were positive for the presence of resistance-associated gene cluster encoding nucleotide-binding and leucine-rich repeat (NL) proteins and known defence genes. Main-effect QTLs for resistance to races 3, 4 and 5 in leaf, stem and pod were located on chromosome 2 within a 3.01-Mb region, where a cluster of nine NL genes was detected. The NL gene Phvul.002G323300 is located in this region, which can be considered an important putative candidate gene for the non-organ-specific QTL identified here. The present research provides essential information not only for the better understanding of the plant-pathogen interaction but also for the application of genomic assisted breeding for halo blight resistance in common bean.     

Construction of a genome-anchored,high-density genetic map for melon (<Emphasis Type="Italic">Cucumis melo</Emphasis> L.) and identification of <Emphasis Type="Italic">Fusarium oxysporum</Emphasis> f. sp. <Emphasis Type="Italic">melonis</Emphasis> race 1 resistance QTL

Key message

Four QTLs and an epistatic interaction were associated with disease severity in response to inoculation with Fusarium oxysporum f. sp. melonis race 1 in a recombinant inbred line population of melon.

Abstract

The USDA Cucumis melo inbred line, MR-1, harbors a wealth of alleles associated with resistance to several major diseases of melon, including powdery mildew, downy mildew, Alternaria leaf blight, and Fusarium wilt. MR-1 was crossed to an Israeli cultivar, Ananas Yok’neam, which is susceptible to all of these diseases, to generate a recombinant inbred line (RIL) population of 172 lines. In this study, the RIL population was genotyped to construct an ultra-dense genetic linkage map with 5663 binned SNPs anchored to the C. melo genome and exhibits the overall high quality of the assembly. The utility of the densely genotyped population was demonstrated through QTL mapping of a well-studied trait, resistance to Fusarium wilt caused by Fusarium oxysporum f. sp. melonis (Fom) race 1. A major QTL co-located with the previously validated resistance gene Fom-2. In addition, three minor QTLs and an epistatic interaction contributing to Fom race 1 resistance were identified. The MR-1 × AY RIL population provides a valuable resource for future QTL mapping studies and marker-assisted selection of disease resistance in melon.

     

Genetic analysis of shoot fresh weight in a cross of wild (<Emphasis Type="Italic">G. soja</Emphasis>) and cultivated (<Emphasis Type="Italic">G. max</Emphasis>) soybean

Shoot fresh weight (SFW) is one of the parameters, used to estimate the total plant biomass yield in soybean. In the present study, a total of 188 F_5:8 recombinant inbred lines (RIL) derived from an interspecific cross of PI 483463 (Glycine soja) and Hutcheson (Glycine max) were investigated for SFW variation in the field for three consecutive years. The parental lines and RILs were phenotyped in the field at the R6 stage by measuring total biomass in kg/plot to identify the QTLs for SFW. Three QTLs qSFW6_1, qSFW15_1, and qSFW19_1 influencing SFW were identified on chromosome 6, 15, and 19, respectively. The QTL qSFW19_1 flanked between the markers BARC-044913-08839 and BARC-029975-06765 was the stable QTL expressed in all the three environments. The phenotypic variation explained by the QTLs across all environments ranged from 6.56 to 21.32 %. The additive effects indicated contribution of alleles from both the parents and additive × environment interaction effects affected the expression of SFW QTL. Screening of the RIL population with additional SSRs from the qSFW19_1 region delimited the QTL between the markers SSR19-1329 and BARC-29975-06765. QTL mapping using bin map detected two QTLs, qSFW19_1A and qSFW19_1B. The QTL qSFW19_1A mapped close to the Dt1 gene locus, which affects stem termination, plant height, and floral initiation in soybean. Potential candidate genes for SFW were pinpointed, and sequence variations within their sequences were detected using high-quality whole-genome resequencing data. The findings in this study could be useful for understanding genetic basis of SFW in soybean.     

Mapping of yield-related QTLs in pepper in an interspecific cross of <Emphasis Type="Italic">Capsicum annuum</Emphasis> and <Emphasis Type="Italic">C. frutescens</Emphasis>

An advanced backcross QTL study was performed in pepper using a cross between the cultivated species Capsicum annuum cv. Maor and the wild C. frutescens BG 2816 accession. A genetic map from this cross was constructed, based on 248 BC(2) plants and 92 restriction fragment length polymorphism (RFLP) markers distributed throughout the genome. Ten yield-related traits were analyzed in the BC(2) and BC(2)S(1) generations, and a total of 58 quantitative trait loci (QTLs) were detected; the number of QTLs per trait ranged from two to ten. Most of the QTLs were found in 11 clusters, in which similar QTL positions were identified for multiple traits. Unlike the high percentage of favorable QTL alleles discovered in wild species of tomato and rice, only a few such QTL alleles were detected in BG 2816. For six QTLs (10%), alleles with effects opposite to those expected from the phenotype were detected in the wild species. The use of common RFLP markers in the pepper and tomato maps enabled possible orthologous QTLs in the two species to be determined. The degree of putative QTL orthology for the two main fruit morphology traits-weight and shape-varied considerably. While all eight QTLs identified for fruit weight in this study could be orthologous to tomato fruit weight QTLs, only one out of six fruit shape QTLs found in this study could be orthologous to tomato fruit shape QTLs.     

Development of breeder-friendly markers for selection of <Emphasis Type="Italic">MIPS1</Emphasis> mutations in soybean

Mutations in the d-myo-inositol 3-phosphate synthase 1 gene (MIPS1) in soybean [Glycine max (L.) Merr.] cause modifications to seed phosphorus and carbohydrate content that improve the nutritional value of food and feed. Molecular markers are an efficient tool for breeding MIPS1 mutant germplasm due to reduced seed germination and field emergence potential. An F₂ population segregating for the MIPS1 mutation found in experimental soybean line V99-5089 was used to develop breeder-friendly markers. Markers were validated in 88 advanced lines from 9 diverse pedigrees. Ten potential simple sequence repeat (SSR) markers, located on Gm11, from the new BARCSOYSSR_1.0 database were tested and four were polymorphic. BARCSOY_11_1495 was 93–97% effective for selecting the mutation. A KBiosciences Competitive Allele Specific PCR (KASPar) assay was developed to select directly for the V99-5089-derived MIPS1 single nucleotide polymorphism (SNP) mutation. The KASPar assay is simple and cost-effective compared to other SNP genotyping assays. The MIPS1 mutation in V99-5089 is likely to have occurred spontaneously. We describe a method of DNA extraction in soybean using a Geno/Grinder for fast and easy tissue maceration.     

Identification of quantitative trait loci for specific mechanisms of resistance to <Emphasis Type="Italic">Orobanche crenata</Emphasis> Forsk. in pea (<Emphasis Type="Italic">Pisum sativum</Emphasis> L.)

Crenate broomrape (Orobanche crenata) is the major constraint for pea cultivation in the Mediterranean Basin and Middle East. Cultivation of resistant varieties would be the most efficient, economical and environmentally friendly way to control this parasite. However, little resistance is available within cultivated pea. Promising sources of resistance have been identified in wild peas but their use in breeding programs is hampered by the polygenic nature of the resistance. The identification of molecular markers linked to the resistance would allow tracking of the underlying genes, facilitating their introgression into pea cultivars. The main objective of this study was the identification of genomic regions associated with resistance to O. crenata. A RIL (Recombinant Inbred Lines) population derived from a cross between a resistant accession of the wild pea Pisum sativum ssp. syriacum, and a susceptible pea variety was screened for resistance to O. crenata under field conditions during two seasons. In addition, resistance reactions at different stages of the O. crenata infection cycle were assessed using a Petri dish method. The approach allowed the identification of four Quantitative Trait Loci (QTL) associated with field resistance, assessed as the number of emerged broomrape shoots per pea plant under field conditions. These identified QTLs explained individually from 10 to 17% of the phenotypic variation. In addition QTLs governing specific mechanisms of resistance, such as low induction of O. crenata seed germination, lower number of established tubercles per host root length unit, and slower development of tubercles were also identified. Identified QTLs explained individually from 8 to 37% of the variation observed depending on the trait. Host plant aerial biomass and root length were also assessed and mapped. Both traits were correlated with the level of O. crenata infection and three out of the four QTLs controlling resistance under field conditions co-localized with QTLs controlling plant aerial biomass or root length. The relationship observed among these traits and resistance is discussed.     

Identification and fine mapping of <Emphasis Type="Italic">qWBPH11</Emphasis> conferring resistance to whitebacked planthopper (<Emphasis Type="Italic">Sogatella furcifera</Emphasis> Horvath) in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

The whitebacked planthopper (WBPH), Sogatella furcifera Horvath, is one of the most destructive pests in rice (Oryza sativa L.) production. Host-plant resistance has been considered as an efficient and eco-friendly strategy to reduce yield losses caused by WBPH. In this study, we found that an indica rice cultivar IR54751-2-44-15-24-2 (IR54751) displayed high resistance to WBPH at both seedling and tillering stages. The resistance of IR54751 was mainly contributed by antixenosis and tolerance rather than antibiosis. An F₂ population derived from a cross between IR54751 and a susceptible japonica cultivar 02428 was constructed to detect the quantitative trait loci (QTLs) conferring the resistance to WBPH. In total, four QTLs including qWBPH3.1, qWBPH3.2, qWBPH11, and qWBPH12 were identified and distributed on three different chromosomes. The four QTLs had LOD scores of 3.8, 8.2, 5.8, and 3.9, accounting for 8.2, 21.5, 13.9, and 10.4% of the phenotypic variation, respectively. Except for qWBPH3.1, the resistance alleles of the other three QTLs were all from IR54751. Further, a secondary population harboring only single qWBPH11 locus was developed from the F₂ population by marker-assisted selection. Finally, qWBPH11 was delimited in a 450-kb region between markers DJ53973 and SNP56. The identification of WBPH resistance QTLs and the fine mapping of qWBPH11 will be helpful for cloning resistance genes and breeding resistant rice cultivars.     

Identification of quantitative trait loci for resistance to <Emphasis Type="Italic">Xanthomonas campestris</Emphasis> pv. <Emphasis Type="Italic">campestris</Emphasis> in <Emphasis Type="Italic">Brassica rapa</Emphasis>

Resistance to six known races of black rot in crucifers caused by Xanthomonas campestris pv. campestris (Pammel) Dowson is absent or very rare in Brassica oleracea (C genome). However, race specific and broad-spectrum resistance (to type strains of all six races) does appear to occur frequently in other brassica genomes including B. rapa (A genome). Here, we report the genetics of broad spectrum resistance in the B. rapa Chinese cabbage accession B162, using QTL analysis of resistance to races 1 and 4 of the pathogen. A B. rapa linkage map comprising ten linkage groups (A01–A10) with a total map distance of 664 cM was produced, based on 223 AFLP bands and 23 microsatellites from a F₂ population of 114 plants derived from a cross between the B. rapa susceptible inbred line R-o-18 and B162. Interaction phenotypes of 125 F₂ plants were assessed using two criteria: the percentage of inoculation sites in which symptoms developed, and the severity of symptoms per plant. Resistance to both races was correlated and a cluster of highly significant QTL that explained 24–64% of the phenotypic variance was located on A06. Two additional QTLs for resistance to race 4 were found on A02 and A09. Markers closely linked to these QTL could assist in the transference of the resistance into different B. rapa cultivars or into B. oleracea.     

The<Emphasis Type="Italic"> Rxo1</Emphasis>/<Emphasis Type="Italic">Rba1</Emphasis> locus of maize controls resistance reactions to pathogenic and non-host bacteria

The genetic mechanism underlying six palatability properties of cooked rice and three physico-chemical traits was dissected in 66 BC₃F₂ chromosome segment substitution lines (CSSLs), using a complete linkage map in three successive years. The CSSLs showed transgressive segregation for all traits studied. Significant correlation was detected among most palatability traits. A total of 25 QTLs for the nine traits were identified on nine chromosomes, and many QTLs affecting different quality traits were mapped in the same regions. Six QTLs—qLT-8 for luster, qTD-6 and qTD-8 for tenderness, qIVOE-6 and qIVOE-8 for integrated value of organoleptic evaluation, and qAC-8 for amylose content—were repeatedly detected across the 3 years. Phenotypic values were significantly different between the recurrent parent, cultivar Asominori, and the CSSLs harboring any of the six QTL alleles across the three environments, indicating that these six QTLs were non-environment-specific and could be used for marker-assisted selection in rice quality improvement.     

Genetic analysis of loci associated with partial resistance to <Emphasis Type="Italic">Sclerotinia sclerotiorum</Emphasis> in rapeseed (<Emphasis Type="Italic">Brassica napus</Emphasis> L.)

Sclerotinia stem rot is the most devastating disease of rapeseed (Brassica napus L.) in China. Quantitative trait loci (QTLs) involved in resistance to Sclerotinia sclerotiorum were detected in a rapeseed population of 128-F(2:3) families derived from a cross between the male sterility restorer line H5200 and a partial resistant line Ning RS-1. A total of 107 molecular markers including 72 RFLPs, 30 AFLPs, 3 SSRs and 2 RAPDs were employed to construct a genetic linkage map with 23 linkage groups covering 1,625.7 cM with an average space of 15.2 cM. Resistance was assessed empirically at two developmental stages: with a detached leaf inoculation at the seedling stage and in vivo stem inoculation at the mature plant stage. The observed resistance was scored for each plant as leaf resistance at the seedling stage (LRS) and stem resistance at the mature plant stage (SRM). A total of 13 loci were identified by one-way ANOVA and six QTLs were detected with MapMaker-QTL. We found that three of the six QTLs were associated with leaf resistance at the seedling stage and collectively accounted for 40.7% of the total phenotypic variation, each accounting for 23.2%, 16.6% and 13.6% respectively. Three QTLs were found corresponding to the disease resistance at the mature plant stage, explaining 49.0% of the phenotypic variation. Epistasis was observed for the resistance and the additive by additive interactions were the predominant type of epistasis. It was concluded that both single-locus QTLs and epistatic interactions played important roles in Sclerotinia resistance in rapeseed.     

Mapping of quantitative trait loci for resistance to <Emphasis Type="Italic">Mycosphaerella pinodes</Emphasis> in <Emphasis Type="Italic">Pisum sativum</Emphasis> subsp. <Emphasis Type="Italic">syriacum</Emphasis>

Aschochyta blight, caused by Mycosphaerella pinodes, is one of the most economically serious pea pathogens, particularly in winter sowings. The wild Pisum sativum subsp. syriacum accession P665 shows good levels of resistance to this pathogen. Knowledge of the genetic factors controlling resistance to M. pinodes in this wild accession would facilitate gene transfer to pea cultivars; however, previous studies mapping resistance to M. pinodes in pea have never included this wild species. The objective of this study was to identify quantitative trait loci (QTL) controlling resistance to M. pinodes in P. sativum subsp. syriacum and to compare these with QTLs previously described for the same trait in P. sativum. A population formed by 111 F_6:7 recombinant inbred lines derived from a cross between accession P665 and a susceptible pea cultivar (Messire) was analysed using morphological, isozyme, RAPD, STS and EST markers. The map developed covered 1214 cM and contained 246 markers distributed in nine linkage groups, of which seven could be assigned to pea chromosomes. Six QTLs associated with resistance to M. pinodes were detected in linkage groups II, III, IV and V, which collectively explained between 31 and 75% of the phenotypic variation depending of the trait. While QTLs MpIII.1 and MpIII.2 were detected both for seedlings and field resistance, MpV.1 and MpII.1 were specific for growth chamber conditions and MpIII.3 and MpIV.1 for field resistance. Quantitative trait loci MpIII.1, MpII.1, MpIII.2 and MpIII.3 may coincide with other QTLs associated with resistance to M. pinodes previously described in P. sativum. Four QTLs associated with earliness of flowering were also identified. While dfIII.2 and dfVI.1, may correspond with other genes and QTLs controlling earliness in P. sativum, dfIII.1 and dfII.1 may be specific to P. sativum subsp. syriacum. Flowering date and growth habit were strongly associated with resistance to M. pinodes in the field evaluations. The relation observed between earliness, growth habit and resistance to M. pinodes is discussed.     

Multiple paternity in <Emphasis Type="Italic">Rhipicephalus</Emphasis> (<Emphasis Type="Italic">Boophilus</Emphasis>) <Emphasis Type="Italic">microplus</Emphasis> confirmed by microsatellite analysis

The aim of this study was to determine if individual ticks among the progeny of a single female Rhipicephalus (Boophilus) microplus tick removed from cattle under natural conditions are the result of mating with one or several males. To this end, simulations were run using an existing dataset of genotypes from 8 microsatellite loci to predict the number of samples required and the best locus. Subsequently, 14–22 progeny from each of 15 engorged female ticks removed from three cows, and the engorged females themselves, were genotyped for the BmM1 locus and the minimum number of potential male parents was determined for each progeny group. Of the 15 progeny groups, 10 must have been sired by more than one male, as indicated by the presence of five unique alleles among the progeny or three unique alleles that could not have been contributed by the female. This finding demonstrates multiple paternity in R. microplus.     

Effect of two vesicular-arbuscular mycorrhizal fungi on the growth of micropropagated potato plantlets and on the extent of disease caused by <Emphasis Type="Italic">Rhizoctonia</Emphasis><Emphasis Type="Italic">solani</Emphasis>

Two micropropagated potato cultivars, Goldrush and LP89221, were inoculated into sowing trays with either Glomus etunicatum or G. intraradices in a greenhouse. After 2 weeks, plantlets were transplanted into pots and roots were challenged 7 days later with Rhizoctonia solani. At different times after R. solani infection, disease severity, mortality rate, root colonization levels, various growth parameters, and shoot mineral content were evaluated. In Goldrush, only inoculation with G. etunicatum led to a significant reduction in disease severity, ranging between 60.2% and 71.2%, on both shoot and crown. This decrease was not observed in LP89221. Compared with the control plantlets, inoculation of Goldrush with G. etunicatum or G. intraradices reduced significantly the mortality rate by 77% and 26%, respectively, whereas vesicular-arbuscular mycorrhizal (VAM) fungi did not significantly influence the mortality rate in LP89221. In Goldrush, inoculation with G. etunicatum significantly increased shoot fresh weight, root dry weight and the number of tubers produced per plant, whereas G. intraradices only significantly increased the number of tubers. Tuber and root fresh weights of both potato cultivars were significantly reduced by R. solani infection. However, R. solani-infected plantlets of both Goldrush and LP89221, inoculated with G. etunicatum, produced significantly greater tuber fresh weight than non-VAM plantlets. In R. solani-infected plantlets of Goldrush but not LP89221, G. etunicatum and G. intraradices increased root fresh weight by approximately 140.3% and 76.5%, respectively, compared with non-VAM plants. The potato cultivars Goldrush and LP89221 responded differently to VAM fungal inoculation and to R. solani infection in terms of shoot mineral content.     

Genetic Overlap in the Quantitative Resistance of Rice at the Seedling and Adult Stages to <Emphasis Type="Italic">Xanthomonas oryzae</Emphasis> pv. <Emphasis Type="Italic">oryzae</Emphasis>

The genetic components responsible for the qualitative and quantitative resistance of rice to three Chinese races (C2, C4, and C5) of Xanthomonas oryzae pv. oryzae (Xoo) were investigated at the seedling and adult stages in two successive years in set of Lemont/Teqing cross introgression lines (ILs) in a Teqing background, to create a complete linkage map using 160 well-distributed SSR markers. Teqing was resistant to C2 and C4, but moderately susceptible to C5, whereas Lemont was susceptible to all three races. Highly significant correlations were detected among the resistance to different races at different developmental stages. A major gene (Xa4), 14 main-effect QTLs (M-QTLs), and 18 epistatic QTLs were identified in the two developmental stages over 2 years, and were largely responsible for the segregation of resistance in the ILs. In 2007, the Lemont alleles at all loci in the seedling stage, except QBbr10 to C4, increased lesion length (LL) or decreased resistance. The Teqing allele at the Xa4 locus acted as a resistance gene against C2 and C4, but acted as a M-QTL when its resistance was overcome by the virulent race C5. M-QTLs showed a degree of race specificity and had a cumulative effect on resistance. Most M-QTLs (94%) consistently expressed resistance to the same race at the seedling and adult stages, indicating that a high degree of genetic overlap exists between Xoo resistance at both developmental stages in rice. Among the digenic interactions, most co-introgressed Lemont alleles at the two epistatic loci lead to significantly smaller LL with all three races, compared to other types of interacting alleles at both development stages. The results indicate that a high level of resistance may be achieved by the cumulative effect of multiple M-QTLs, including the residual effects of “defeated” major resistance genes and the epistatic effects of co-introgression from diverse susceptible varieties.