Use In Marker-assisted Selection Research Articles

Mapping and characterization QTLs for phenological traits in seven pedigree-connected peach families

BackgroundEnvironmental adaptation and expanding harvest seasons are primary goals of most peach [Prunus persica (L.) Batsch] breeding programs. Breeding perennial crops is a challenging task due to their long breeding cycles and large tree size. Pedigree-based analysis using pedigreed families followed by haplotype construction creates a platform for QTL and marker identification, validation, and the use of marker-assisted selection in breeding programs.ResultsPhenotypic data of seven F1 low to medium chill full-sib families were collected over 2 years at two locations and genotyped using the 9 K SNP Illumina array. Three QTLs were discovered for bloom date (BD) and mapped on linkage group 1 (LG1) (172–182 cM), LG4 (48–54 cM), and LG7 (62–70 cM), explaining 17–54%, 11–55%, and 11–18% of the phenotypic variance, respectively. The QTL for ripening date (RD) and fruit development period (FDP) on LG4 was co-localized at the central part of LG4 (40–46 cM) and explained between 40 and 75% of the phenotypic variance. Haplotype analyses revealed SNP haplotypes and predictive SNP marker(s) associated with desired QTL alleles and the presence of multiple functional alleles with different effects for a single locus for RD and FDP.ConclusionsA multiple pedigree-linked families approach validated major QTLs for the three key phenological traits which were reported in previous studies across diverse materials, geographical distributions, and QTL mapping methods. Haplotype characterization of these genomic regions differentiates this study from the previous QTL studies. Our results will provide the peach breeder with the haplotypes for three BD QTLs and one RD/FDP QTL to create predictive DNA-based molecular marker tests to select parents and/or seedlings that have desired QTL alleles and cull unwanted genotypes in early seedling stages.

High-Density Genetic Linkage Map Construction and White Rot Resistance Quantitative Trait Loci Mapping for Genus Vitis Based on Restriction Site-Associated DNA Sequencing.

Grape white rot (Coniothyrium diplodiella) is a major fungal disease affecting grape yield and quality. Quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits of grapevine. This study was conducted to construct a high-density map and conduct QTL mapping for grapevine white rot resistance. A mapping population with 177 genotypes was developed from interspecific hybridization of a white rot-resistant cultivar (Vitis vinifera × V. labrusca 'Zhuosexiang') and white rot-susceptible cultivar (V. vinifera 'Victoria'). Single-nucleotide polymorphism (SNP) markers were developed by restriction site-associated DNA sequencing. The female, male, and integrated maps contained 2,501, 4,110, and 6,249 SNP markers with average genetic distances of adjacent markers of 1.25, 0.77, and 0.50 cM, respectively. QTL mapping was conducted based on white rot resistance identification of 177 individuals in July and August of 2017 and 2018. Notably, one stable QTL related to white rot resistance was detected and located on linkage group LG14. The phenotypic variance ranged from 12.93 to 13.43%. An SNP marker (chr14_3929380), which cosegregated with white rot resistance, was discovered and shows potential for use in marker-assisted selection to generate new grapevine cultivars with resistance to white rot.

Association Mapping of Verticillium Wilt Disease in a Worldwide Collection of Cotton (Gossypium hirsutum L.).

Cotton (Gossypium spp.) is the best plant fiber source in the world and provides the raw material for industry. Verticillium wilt caused by Verticillium dahliae Kleb. is accepted as a major disease of cotton production. The most practical way to deal with verticillium wilt is to develop resistant/tolerant varieties after cultural practices. One of the effective selections in plant breeding is the use of marker-assisted selection (MAS) via quantitative trait loci (QTL). Therefore, in this study, we aimed to discover the genetic markers associated with the disease. Through the association mapping analysis, common single nucleotide polymorphism (SNP) markers were obtained using 4730 SNP alleles. As a result, twenty-three markers were associated with defoliating (PYDV6 isolate) pathotype, twenty-one markers with non-defoliating (Vd11 isolate) pathotype, ten QTL with Disease Severity Index (DSI) of the leaves at the 50–60% boll opening period and eight markers were associated with DSI in the stem section. Some of the markers that show significant associations are located on protein coding genes such as protein Mpv17-like, 21 kDa protein-like, transcription factor MYB113-like, protein dehydration-induced 19 homolog 3-like, F-box protein CPR30-like, extracellular ribonuclease LE-like, putative E3 ubiquitin-protein ligase LIN, pentatricopeptide repeat-containing protein At3g62890-like, fructose-1,6-bisphosphatase, tubby-like F-box protein 8, endoglucanase 16-like, glucose-6-phosphate/phosphate translocator 2, metal tolerance protein 11-like, VAN3-binding protein-like, transformation/transcription domain-associated protein-like, pyruvate kinase isozyme A, ethylene-responsive transcription factor CRF2-like, molybdate transporter 2-like, IRK-interacting protein-like, glycosylphosphatidylinositol anchor attachment 1 protein, U3 small nucleolar RNA-associated protein 4-like, microtubule-associated protein futsch-like, transport and Golgi organization 2 homolog, splicing factor 3B subunit 3-like, mediator of RNA polymerase II transcription subunit 15a-like, putative ankyrin repeat protein, and protein networked 1D-like. It has been reported in previous studies that most of these genes are associated with biotic and abiotic stress factors. As a result, once validated, it would be possible to use the markers obtained in the study in Marker Assisted Selection (MAS) breeding.

Prototype for developing SNP markers from GWAS and biparental QTL for rice panicle and grain traits

AbstractThere is a large gap between genomewide association studies (GWAS) and developing markers that can be used in marker‐assisted selection (MAS) schemes for cultivar improvement. This study is a prototype for developing markers using segregating single nucleotide polymorphisms (SNPs) for panicle architecture and grain shape traits identified by GWAS in the Rice Diversity Panel‐1 and colocalized in QTL regions revealed by linkage mapping in the Estrela × NSFTV199 rice (Oryza sativa L.) population. Markers were developed from sequence variants suitable for reliable detection in regions surrounding the most significant SNPs identified in GWAS. Once developed, the markers were validated in three Japonica subspecies biparental populations, used to improve QTL mapping resolution, and employed to select potential parents for use in MAS. All marker alleles segregated in the rice tropical japonica subpopulation.

Quarantine nematode species and pathotypes potentially dangerous for domestic potato production: populations diversity and the genetics of potato resistance

Обзор посвящен проблеме потенциально опасных для отечественного картофелеводства каран- тинных видов и патотипов нематод. Картофель поражают более 30 видов паразитических нематод, однако в статье основное внимание уделено самым вредоносным, приносящим большой ущерб картофелеводству пред- ставителям родов Globodera, Ditylenchus, Nacobbus и Meloidogyne. Проанализированы фитопатологические и молекулярные методы идентификации видов и патотипов и основные достижения в изучении изменчивости популяций паразитических нематод картофеля. Показано, что, благодаря особенностям жизненного цикла не- матод и лабильности их геномов, генетическая изменчивость этих организмов очень велика, что создает угрозу образования новых патогенных генотипов паразита. Сведения о внутри- и межпопуляционной изменчивости нематод важны для изучения путей интродукции и распространения отдельных видов, а также поиска корреля- ций молекулярных маркеров с определенным патотипом. Филогенетические исследования, основанные на со- временных данных по генетической изменчивости популяций, позволили выявить комплексы видов у Globodera pallida (Stone) Behrens и Nacobbus aberrans (Thorne) Thorne & Allen (sensu lato), включающие криптические виды. К основным составляющим успешной защиты, предотвращающей массовое распространение паразитических нематод, относятся карантинные мероприятия, агротехнические приемы, биологические способы защиты и возделывание устойчивых сортов. Особое внимание в обзоре уделено вопросам селекции сортов картофеля с длительной устойчивостью к различным видам нематод, поскольку возделывание таких сортов – экологически наиболее безопасный и экономически выгодный способ предотвращения эпифитотий. В настоящее время до- стигнуты значительные успехи в генетической защите сортов картофеля, особенно в отношении цистообразую- щих нематод. Приведены сведения об источниках устойчивости картофеля к паразитическим нематодам, выде- ленных в коллекциях диких и культурных видов. Проанализированы данные об идентифицированных R-генах и QTL устойчивости, которые были интрогрессированы в селекционный материал с помощью различных методов и подходов. Представлены результаты изучения структурной и функциональной организации генов устойчиво- сти к цистообразующим нематодам картофеля. Рассмотрены результаты исследований по использованию моле- кулярных маркеров определенных генов в маркер-опосредованной селекции для создания новых устойчивых сортов, в том числе с групповой устойчивостью.

ON USING DATA FROM MARKER-ASSISTED SELECTION OF SOURCE MATERIAL AND INTERVARIETAL HYBRIDS IN PRACTICAL POTATO BREEDING

The success of breeding research is in many ways determined by the successful selection of parental forms for hybridization. In recent years, along with traditional approaches, the results of marker-assisted selection (MAS) are actively used for the selection of parental lines, in order to combine valuable alleles of parental genotypes. Such programs are widely used for different crops in many countries, including Russia. The use of MAS is promising both at the initial stage in the selection of parental samples for crosses and at the stages of analysis of segregating hybrid populations. In this work, the selection of parental potato varieties for crosses was carried out based on the results of MAS of initial varieties with markers of R-genes conferring resistance to various harmful organisms as well as based on their economically valuable characters. To increase the efficiency of the selection of promising hybrid genotypes obtained in intervarietal crosses, we used an integrated approach that combines MAS with markers of R-genes for resistance to various diseases and pests with traditional methods for assessing economically valuable traits of hybrid populations. The resulting hybrids of three combinations (Gusar × Charoit), (Gusar × Aliy Parus), (Gusar × Sireneviy tuman) also participated in MAS with 8 markers of 6 R-genes conferring resistance to potato virus Y (Rysto) and potato virus X (Rx1), to golden (H1) and pale (Gpa2) potato cyst nematodes, and race-specific resistance to late blight (R1, R3A). Almost all the hybrids had different combinations of R-gene markers. To identify the allelic composition of the R-genes in the parental varieties, the segregation of DNA markers in each combination was analyzed, which allowed us to determine the level of heterozygosity of the marked loci in the parental varieties. Main economically valuable characters of the hybrids were also evaluated in the field trials. As a result, out of 144 hybrids, 31 genotypes were identified that have one or the other economically valuable traits (yield, marketability, shape of tubers, starch content, field resistance to late blight), and 113 hybrids were rejected. In 23 of the 31 selected hybrids, productivity varied from 600 to 1525 grams per plant. Twelve of these 23 hybrid genotypes combined relatively high productivity and marketability of tubers with various combinations of Rysto, Rx1, H1, Gpa2, R1, and R3A gene markers. Thus, the use of an integrated approach that combines traditional breeding methods and MAS increases the efficiency of the selection of promising genotypes with a given set of traits.The selected hybrid genotypes are of interest for further breeding aimed at creating competitive varieties with complex resistance to various pathogens and pests, including viral and nematode resistance, that will need fewer chemical treatments to protect the crop.

ИСПОЛЬЗОВАНИЕ В ПРАКТИЧЕСКОЙ СЕЛЕКЦИИ КАРТОФЕЛЯ РЕЗУЛЬТАТОВ ДНК-МАРКИРОВАНИЯ ИСХОДНЫХ РОДИТЕЛЬСКИХФОРМ И МЕЖСОРТОВЫХ ГИБРИДОВ

The success of breeding research is in many ways determined by the successful selection of parental forms for hybridization. In recent years, along with traditional approaches, the results of marker-assisted selection (MAS) are actively used for the selection of parental lines, in order to combine valuable alleles of parental genotypes. Such programs are widely used for different crops in many countries, including Russia. The use of MAS is promising both at the initial stage in the selection of parental samples for crosses and at the stages of analysis of segregating hybrid populations. In this work, the selection of parental potato varieties for crosses was carried out based on the results of MAS of initial varieties with markers of R-genes conferring resistance to various harmful organisms as well as based on their economically valuable characters. To increase the efficiency of the selection of promising hybrid genotypes obtained in intervarietal crosses, we used an integrated approach that combines MAS with markers of R-genes for resistance to various diseases and pests with traditional methods for assessing economically valuable traits of hybrid populations. The resulting hybrids of three combinations (Gusar × Charoit), (Gusar × Aliy Parus), (Gusar × Sireneviy tuman) also participated in MAS with 8 markers of 6 R-genes conferring resistance to potato virus Y (Rysto) and potato virus X (Rx1), to golden (H1) and pale (Gpa2) potato cyst nematodes, and race-specific resistance to late blight (R1, R3A). Almost all the hybrids had different combinations of R-gene markers. To identify the allelic composition of the R-genes in the parental varieties, the segregation of DNA markers in each combination was analyzed, which allowed us to determine the level of heterozygosity of the marked loci in the parental varieties. Main economically valuable characters of the hybrids were also evaluated in the field trials. As a result, out of 144 hybrids, 31 genotypes were identified that have one or the other economically valuable traits (yield, marketability, shape of tubers, starch content, field resistance to late blight), and 113 hybrids were rejected. In 23 of the 31 selected hybrids, productivity varied from 600 to 1525 grams per plant. Twelve of these 23 hybrid genotypes combined relatively high productivity and marketability of tubers with various combinations of Rysto, Rx1, H1, Gpa2, R1, and R3A gene markers. Thus, the use of an integrated approach that combines traditional breeding methods and MAS increases the efficiency of the selection of promising genotypes with a given set of traits.The selected hybrid genotypes are of interest for further breeding aimed at creating competitive varieties with complex resistance to various pathogens and pests, including viral and nematode resistance, that will need fewer chemical treatments to protect the crop.

Genome-Wide Association Mapping of Seedling Drought Tolerance in Winter Wheat.

In the southern Great Plains of the United States, winter wheat grown for dual-purpose is often planted early, which puts it at risk for drought stress at the seedling stage in the autumn. To map quantitative trait loci (QTL) associated with seedling drought tolerance, a genome-wide association study (GWAS) was performed on a hard winter wheat association mapping panel. Two sets of plants were planted in the greenhouse initially under well-watered conditions. At the five-leaf stage, one set continued to receive the optimum amount of water, whereas watering was withdrawn from the other set (drought stress treatment) for 14 days to mimic drought stress. Large phenotypic variation was observed in leaf chlorophyll content, leaf chlorophyll fluorescence, shoot length, number of leaves per seedling, and seedling recovery. A mixed linear model analysis detected multiple significant QTL associated with seedling drought tolerance-related traits on chromosomes 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4B, 5A, 5B, 6B, and 7B. Among those, 12 stable QTL responding to drought stress for various traits were identified. Shoot length and leaf chlorophyll fluorescence were good indicators in responding to drought stress because most of the drought responding QTL detected using means of these two traits were also detected in at least two experimental repeats. These stable QTL are more valuable for use in marker-assisted selection during wheat breeding. Moreover, different traits were mapped on several common chromosomes, such as 1B, 2B, 3B, and 6B, and two QTL clusters associated with three or more traits were located at 107–130 and 80–83 cM on chromosomes 2B and 6B, respectively. Furthermore, some QTL detected in this study co-localized with previously reported QTL for root and shoot traits at the seedling stage and canopy temperature at the grain-filling stage of wheat. In addition, several of the mapped chromosomes were also associated with drought tolerance during the flowering or grain-filling stage in wheat. Some significant single-nucleotide polymorphisms (SNPs) were aligned to candidate genes playing roles in plant abiotic stress responses. The SNP markers identified in this study will be further validated and used for marker-assisted breeding of seedling drought tolerance during dual-purpose wheat breeding.

Identification of SSR markers for Fusarium head blight resistance in durum and bread wheat

In the present study, 25 durum and 25 bread wheat genotypes were evaluated during 2016 and 2017 for Fusarium head blight (FHB) resistance under greenhouse conditions. FHB severity ranged from 10.33% to 94.20%. Highly significant (p < 0.01) genotypes differences were observed, indicating abundant genetic variability. High broad-sense heritability (0.87) and high genetic advance (70.3%) were obtained for FHB severity, suggesting considerable genetic improvement by selection. Of 50 genotypes tested, 6 genotypes showed <20%, 20 genotypes had >50%, and 24 genotypes showed 20–50% disease severity. The most resistant genotypes were BeniSuef-5, Sohag-3, Ciccio, Svevo, WA-88 and Misr-1 with average FHB severity of 10.84, 11.42, 11.49, 14.09, 16.03 and 18.69%, respectively, suggesting the presence of FHB resistance genes. On average, durum wheat genotypes showed lower FHB severity (39.9%) compared to bread wheat (49.1%). Of 18 simple sequence repeat (SSR) markers tested, Xgwm292-5A and Xgwm533-3B could be considered as markers associated with FHB resistance in the tested genotypes. However, further molecular analysis would be performed to confirm their usefulness for marker-assisted selection in wheat breeding programs.

Combined linkage mapping and association analysis reveals genetic control of maize kernel moisture content.

The free moisture in crop kernels after being naturally dried is referred to as kernel moisture content (KMC). Maize KMC reflects grain quality and influences transportation and storage of seeds. We used an IBM Syn10 DH maize population consisting of 249 lines and an association panel comprising 310 maize inbred lines to identify the genetic loci affecting maize KMC in three environments. Using the IBM population detected 13 QTL on seven chromosomes, which were clustered into nine common QTL. Genome-wide association analysis (GWAS) identified 16 significant SNPs across the 3 environments, which were linked to 158 genes across the three environments. Combined QTL mapping and GWAS found two SNPs that were located in two of the mapped QTL, respectively. Twenty-three genes were linked with the loci co-localized in both populations. Of these 181 genes, five have previously been reported to be associated with KMC or to regulate seed development. These associations were verified by candidate gene association analysis. Two superior alleles and one favorable haplotype for Zm00001d007774 and Zm00001d047868 were found to influence KMC. These findings provide insights into molecular mechanisms underlying maize KMC and contribute to the use of marker-assisted selection for breeding low-KMC maize.

Meta-analysis of QTL reveals the genetic control of yield-related traits and seed protein content in pea

Pea is one of the most important grain legume crops in temperate regions worldwide. Improving pea yield is a critical breeding target. Nine inter-connected pea recombinant inbred line populations were evaluated in nine environments at INRAE Dijon, France and genotyped using the GenoPea 13.2 K SNP array. Each population has been evaluated in two to four environments. A multi-population Quantitative Trait Loci (QTL) analysis for seed weight per plant (SW), seed number per plant (SN), thousand seed weight (TSW) and seed protein content (SPC) was done. QTL were then projected on the multi-population consensus map and a meta-analysis of QTL was performed. This analysis identified 17 QTL for SW, 16 QTL for SN, 35 QTL for TSW and 21 QTL for SPC, shedding light on trait relationships. These QTL were resolved into 27 metaQTL. Some of them showed small confidence intervals of less than 2 cM encompassing less than one hundred underlying candidate genes. The precision of metaQTL and the potential candidate genes reported in this study enable their use for marker-assisted selection and provide a foundation towards map-based identification of causal polymorphisms.

Exploring physiological and genetic variation of digital cushion thickness in Holstein and Jersey cows and bulls

The objectives of our study were to expand phenotypic characterization of digital cushion thickness (DCT) to the Jersey breed and include mature bulls and to identify breed-specific quantitative trait loci (QTL) for DCT within the Jersey or Holstein breeds and common QTL across breeds and sexes to better understand biological regulation and guide future use of marker-assisted selection. In a cohort of 698 cows and 85 bulls (Holstein and Jersey) from 8 farms in New York State, data were collected on DCT, body condition score (BCS), withers height, and sacral height. All animals underwent sonographic examination of the digital cushion evaluated at the sole ulcer site for the right front and hind feet. Linear mixed models were conducted on DCT separately for cows and bulls with fixed effects of time point, breed, age, digit, and BCS group. The models included random effects to control for the random subset of animals per farm, repeated measures, and multiple measurements from each animal. The phenotypic results indicated that DCT varied by time point, breed, age, digit, and BCS group for cows and by breed, age, digit, and BCS group for bulls. For the genotypic study, 616 cow DNA samples were genotyped on the Illumina BovineHD 777K BeadChip (Illumina Inc., San Diego, CA), whereas 76 bull DNA samples were genotyped on different platforms ranging from 5K to 150K. Multiple genome-wide association studies were conducted to highlight pertinent phenotyping parameters and genetic markers for genomic selection. Data were separated into 8 data sets based on different combinations of breed and sex. Each data set was assessed for quality of markers and samples before conducting genome-wide association studies for DCT, testing the inheritance models and genetic variation of digit, foot, and average thickness. Ten markers passed the Bonferroni correction threshold and 9 passed false discovery rate from 10 genome-wide association studies using a combination of the covariates breed, sex, genotyping batch plate, age, BCS, withers height, and sacral height. Of the 43 candidate genes, 8 novel biologically plausible genes were identified on Bos taurus autosomes 3, 4, 7, and 9: SFRS18 and LRRFIP1 function in fat deposition, whereas AHR, BZW2, EFNA5, USP45, and VAV3 effect bone growth, and SOSTDC1 is related to epidermal keratinocyte function. The genetic markers associated with DCT in this study were explored for variation between cows and bulls within and across breeds for their potential use in marker-assisted selection.

Validation of an Associative Transcriptomics platform in the polyploid crop species Brassica juncea by dissection of the genetic architecture of agronomic and quality traits

The development of more productive crops will be key to addressing the challenges that climate change, population growth and diminishing resources pose to global food security. Advanced 'omics techniques can help to accelerate breeding by facilitating the identification of genetic markers for use in marker-assisted selection. Here, we present the validation of a new Associative Transcriptomics platform in the important oilseed crop Brassica juncea. To develop this platform, we established a pan-transcriptome reference for B. juncea, to which we mapped transcriptome data from a diverse panel of B. juncea accessions. From this panel, we identified 355050 single nucleotide polymorphism variants and quantified the abundance of 93963 transcripts. Subsequent association analysis of functional genotypes against a number of important agronomic and quality traits revealed a promising candidate gene for seed weight, BjA.TTL, as well as additional markers linked to seed colour and vitamin E content. The establishment of the first full-scale Associative Transcriptomics platform for B. juncea enables rapid progress to be made towards an understanding of the genetic architecture of trait variation in this important species, and provides an exemplar for other crops.

Marker-Assisted Selection of Trees with MALE STERILITY 1 in Cryptomeria japonica D. Don

The practical use of marker-assisted selection (MAS) is limited in conifers because of the difficulty with developing markers due to a rapid decrease in linkage disequilibrium, the limited genomic information available, and the diverse genetic backgrounds among the breeding material collections. First, in this study, two families were produced by artificial crossing between two male-sterile trees, ‘Shindai11’ and ‘Shindai12’, and a plus tree, ‘Suzu-2’ (Ms1/ms1) (S11-S and S12-S families, respectively). The segregation ratio between the male-sterile and male-fertile trees did not deviate significantly from the expected 1:1 ratio in either family. These results clearly suggested that the male-sterile gene of ‘Shindai11’ and ‘Shindai12’ is MALE STERILITY 1 (MS1). Since it is difficult to understand the relative positions of each marker, due to the lack of a linkage map which all the closely linked markers previously reported are mapped on, we constructed a partial linkage map of the region encompassing MS1 using the S11-S and S12-S families. For the S11-S and S12-S families, 19 and 18 markers were mapped onto the partial linkage maps of the MS1 region, respectively. There was collinearity (conserved gene order) between the two partial linkage maps. Two markers (CJt020762_ms1-1 and reCj19250_2335) were mapped to the same position as the MS1 locus on both maps. Of these markers, we used CJt020762 for the MAS in this study. According to the MAS results for 650 trees from six prefectures of Japan (603 trees from breeding materials and 47 trees from the Ishinomaki natural population), five trees in Niigata Prefecture and one tree in Yamagata Prefecture had heterozygous ms1-1, and three trees in Miyagi Prefecture had heterozygous ms1-2. The results obtained in this study suggested that ms1-1 and ms1-2 have different geographical distributions. Since MAS can be used effectively to reduce the labor and time required for selection of trees with a male-sterile gene, the research should help ensure that the quantity of breeding materials will increase to assist future tree-breeding efforts.

Identification of QTLs for Resistance to Fusarium Head Blight Using a Doubled Haploid Population Derived from Southeastern United States Soft Red Winter Wheat Varieties AGS 2060 and AGS 2035.

Fusarium head blight (FHB), caused primarily by the fungus Fusarium graminearum, is one of the most damaging diseases of wheat, causing significant loss of yield and quality worldwide. Warm and wet conditions during flowering, a lack of resistant wheat varieties, and high inoculum pressure from corn stubble contribute to frequent FHB epidemics in the southern United States. The soft red winter wheat variety AGS 2060 is moderately susceptible (as opposed to susceptible) to FHB and regularly found in pedigrees of resistant breeding lines. AGS 2060 does not carry any known resistance genes or quantitative trait loci (QTL). A QTL mapping study was conducted to determine the location and genetic effect of its resistance using a doubled haploid mapping population produced from a cross between wheat varieties AGS 2060 and AGS 2035 (FHB susceptible). The population was genotyped using the Illumina iSelect single nucleotide polymorphism (SNP) array for wheat and phenotyped in Baton Rouge and Winnsboro, Louisiana and Newport, Arkansas in 2018 and 2019. The effect of genotype was significant for Fusarium damaged kernels (FDK) and deoxynivalenol (DON) content across all locations and years, indicating genetic variation in the population. The study detected 13 QTLs (one each on chromosome 1A, 1B, 1D, 2A, 2B, 6A, 6B, 7A, and 7B, and two each on 5A and 5B) responsible for the reduction of FDK and/or DON. Of these, nine QTLs for FHB resistance were identified in Winnsboro, Louisiana, in 2019. QTLs on chromosomes 2A and 7A could be valuable sources of resistance to both DON and FDK over several environments and were likely the best candidates for use in marker-assisted selection. Consistently expressed QTLs on chromosomes 5A, 6B, and 7A were potentially newly identified sources of resistance to FHB in soft red winter wheat.

Molecular Marker Development and Gene Cloning for Diverse Disease Resistance in Pepper (Capsicum annuum L.): Current Status and Prospects

The production of chili pepper (Capsicum annuum L.) is hindered by several biotic factors even though striding progresses were made in genetic improvement in the last two decades. Among the advancements were the fast-track genetic improvement of disease-resistant varieties by the use of marker-assisted selection (MAS) and the conventional breeding-based introgression of major resistance genes. Marker development, marker-based identification and fine mapping have revealed a large number of resistance genes, from which cloning of some candidate genes demonstrated the applicability and versatility of map-based cloning for disease resistance. In some of the recent fine mapping of disease resistance QTLs, closely linked DNA markers were identified, which in turn resulted in the rapid introgression of target gene(s) into breeding lines. Also, progresses were made on the characterization and map-based cloning of resistance genes conferring broad-spectrum resistance. As the number of identified and characterized resistance genes and the DNA markers linked to resistance genes are steadily generated, the development of multiple/durable resistance to major chili pepper diseases is accelerated by MAS. In the present review, the development of molecular markers, marker-based mapping of genes conferring resistance to ten major chili pepper diseases were discussed, focusing on the recent advancements in major and QTL-spanning resistance gene mapping. The review provides up-to-date insights into the development of DNA markers linked to disease resistance genes and the cloning of resistance genes, which are all so crucial in pepper breeding for disease resistance.

Dissection of quantitative trait loci for root characters and day length sensitivity in SynOpDH wheat (Triticum aestivum L.) bi-parental mapping population

AbstractThe genetics of the root system is still not dissected for wheat and lack of knowledge prohibits the use of marker-assisted selection in breeding. To understand the genetic mechanism of root development, Synthetic W7984 × Opata M85 doubled-haploid (SynOpDH) mapping population was evaluated for root and shoot characteristics in PVC tubes until maturity. Two major quantitative trait loci (QTLs) for total root biomass were detected on homoeologous chromosomes 2A and 2D with logarithm of the odds scores between 6.25–10.9 and 11.8–20.86, and total phenotypic effects between 12.7–17.7 and 26.6–40.04% in 2013 and 2014, respectively. There was a strong correlation between days to anthesis and root and shoot biomass accumulation (0.50–0.81). The QTL for biomass traits on chromosome 2D co-locates with QTL for days to anthesis. The effect of extended vegetative growth, caused by photoperiod sensitivity (Ppd) genes, on biomass accumulation was always hypothesized, this is the first study to genetically support this theory.

Development and Application of a Multiplex Marker Assay to Detect PVY Resistance Genes in Solanum tuberosum

Potato virus Y (PVY) is a major pathogen affecting potato production worldwide. Three independent genes (Ryadg,Rysto,and Rychc) conferring genetic resistance to all known strains of the virus are currently utilized by breeding programs to develop potato varieties containing extreme resistance to infection by PVY. These resistance genes are typically detected using primers specific for the generation of markers closely-linked to the resistance genes. In recent years there have been attempts to develop a multiplex PCR assay for all resistance genes, but all current published methods either omit at least one resistance gene or are unnecessarily complex and therefore difficult to incorporate successfully for marker-assisted selection. We have developed an assay which tests for the presence of all three sources of resistance in a single, easy to use PCR protocol. The multiplex PCR assay was applied to potato varieties, second-field year breeding germplasm, and a selection of test crosses having progeny segregating for multiple resistance genes to validate the methodology for use in marker-assisted selection in potato breeding programs.

Retracted: Verification of single nucleotide polymorphism (SNP) markers associated with maize (Zea mays. L) streak virus resistance in early generation maize lines

Maize streak virus (MSV) is a devastating viral disease of maize in sub-Saharan Africa. The disease may cause up to 100% yield loss in susceptible crops. The use of molecular markers can facilitate the development of varieties resistant to the virus. The objective of this study is to assess the usefulness of Single Nucleotide Polymorphism (SNP) markers linked to MSV resistance in selecting for resistance at early generations of inbred line development in maize. A total of 160 maize lines were genotyped with three SNP markers that are linked to MSV resistance. These lines were tested for their reaction to MSV through artificial inoculation using viruliferous Cicadulina triangular at the three leaf stage; maize streak virus symptom was scored from 7 days after inoculation for six weeks at weekly interval on a scale of 1 to 5. MSV titer on the upper and lower leaves was determined using Direct Antigen Coating Enzyme linked Immunosorbent Assay (DAC-ELISA). One hundred and forty-two (142) of the 160 maize lines had the favourable marker allele for MSV resistance while 18 maize lines did not have the allele. Differences among the 160 maize lines for MSV symptom on upper leaves at six week after inoculation were significant (P< 0.01). Favourable allele of the SNP markers was significantly associated with MSV symptom score at 6 week after inoculation and MSV titer status. The percentage of maize lines with desirable marker allele with resistance based on symptoms score and ELISA were 97.9 and 93%, respectively. The three SNP markers showed high efficiency in the identification of MSV resistant maize lines and therefore have potential for use in marker-assisted selection. The SNP markers were not effective in detecting MSV resistance in few genotypes, indicating a need to develop other markers for resistance. Key words: ELISA, genotyping, inoculation, maize streak virus, SNPs. See: Notice of Retraction

Four Consistent Loci Confer Adult Plant Resistance to Leaf Rust in the Durum Wheat Lines Heller#1 and Dunkler.

The durum wheat lines Heller#1 and Dunkler from the International Maize and Wheat Improvement Center Global Wheat Program showed moderate and stable adult plant resistance to leaf rust under high disease pressure over field environments in northwestern Mexico. Leaf rust phenotyping was performed on two recombinant inbred line (RIL) populations derived from crosses of Heller#1 and Dunkler with the susceptible parent Atred#2, conducted under artificially induced Puccinia triticina epidemics in 2013, 2014, 2015, and 2016. The Atred#2 × Heller#1 and Atred#2 × Dunkler populations were genotyped by single nucleotide polymorphism (SNP) platforms and diversity arrays technology markers, respectively. Four leaf rust resistance quantitative trait loci were detected simultaneously in the two RIL populations: Lr46, QLr.cim-2BC, QLr.cim-5BL, and QLr.cim-6BL based on phenotypic data across all four crop seasons. They explained 11.7 to 46.8%, 7.2 to 26.1%, 8.4 to 24.1%, and 12.4 to 28.5%, respectively, of the phenotypic variation for leaf rust resistance in Atred#2 × Heller#1 and 16.3 to 56.6%, 6.7 to 15.7%, 4.1 to 10.1%, and 5.1 to 20.2% of the variation in the Atred#2 × Dunkler population. Only the resistance allele of QLr.cim-2BC was from the susceptible parent Atred#2, and resistance alleles at other loci came from the resistant parents Heller#1 and Dunkler. The SNP markers closely linked to Lr46 and QLr.cim-2BC were converted to kompetitive allele specific PCR markers for use in marker-assisted selection to improve leaf rust resistance through crosses with Heller#1 and Dunkler sources.