SSR Genotyping Research Articles

First report of Ug99 Wheat Stem Rust caused by Puccinia graminis f. sp. tritici in South Asia.

Since the emergence of Ug99 wheat stem rust in Uganda in 1998 (Pretorius et al. 2000), the threat of movement into South Asia has been a concern due to long-distance dispersal capacity of airborne spores (Brown and Hovmøller 2002; Singh et al. 2008; Meyer et al. 2017). Increased preparedness by comprehensive rust surveillance efforts and development and deployment of resistant cultivars in advance of an incursion into South Asia has been one of the success stories of the Borlaug Global Rust Initiative (Sharma et al. 2013). In November 2023, an off-season rust survey was conducted in Marpha, Gandaki and Bagmati provinces in Nepal. Rust was only observed at two sites, Dangdunge of Dolakha district and Mude of Sindhupalchok district, where spring wheat was grown as fodder crop outside the main cropping season. Rust infected wheat leaves (10-15 leaves per site) were air dried and sealed in envelopes that were shipped under permit to the Global Rust Reference Center, Denmark. Bulk samples of stem rust, Puccinia graminis f.sp. tritici (Pgt), were recovered from both envelopes, and single pustule isolates were raised and multiplied on Morocco and McNair. Meanwhile, specimens of dry leaves were subjected to SSR genotyping according to standard procedures (Patpour et al. 2022). One distinct multi-locus Pgt genotype was observed, identical to and representing 99% of Ug99 isolates within Clade I collected in East Africa between 2012-2022. A Pgt single pustule isolate from each of the sampling sites were inoculated onto 20 internationally agreed stem rust differential lines using standard procedures, and 14 supplementary lines providing additional resolution of pathogen virulence (Patpour et al. 2022). The pathotyping was repeated in two independent experiments, which resulted in the infection type pattern of Pgt race TTKTT (Supplementary Table 1). Additional independent SSR genotype assays of recovered isolates confirmed the prevalent genotype of Clade I (Patpour et al. 2022; Szabo et al. 2022). This first detection of Ug99 race TTKTT in South Asia emphasizes the need for continued coordinated international surveillance efforts and utilization of diverse sources of resistance to control stem rust in wheat. New surveillance efforts in Nepal during February-March 2024 did not reveal additional cases of wheat stem rust. However, more detailed and sustained rust surveillance efforts, assessment of the vulnerability of current wheat crops to Ug99 and other races of stem-, stripe/yellow- and leaf rust, as well as intensified breeding for rust resistance throughout the region is strongly recommended to meet current and future plant health risks.

Location and differentiation of chestnut tree (Castanea sativa Mill.) individuals grafted with traditional cultivars using spatio-temporal analysis of remote-sensed imagery, dendro-chronological analysis, and SSR genotyping

Location and differentiation of chestnut tree (<i>Castanea sativa</i> Mill.) individuals grafted with traditional cultivars using spatio-temporal analysis of remote-sensed imagery, dendro-chronological analysis, and SSR genotyping

SSR-BASED ASSESSMENT OF GENETIC DIVERSITY IN TOMATO CULTIVARS AND LINES GROWN IN KAZAKHSTAN

Tomato (Solanum lycopersicum L.) is a versatile crop known for its nutritional value and health benefits, thriving in diverse climates worldwide. Nevertheless, regional variations persist in tomato yield, with Kazakhstan serving as an example of lower productivity in contrast to global averages. Closing this disparity requires comprehensive genetic studies and breeding efforts. This study is focused on the genetic diversity of 49 tomato cultivars and hybrids sourced from Kazakh Research Institute of Fruit and Vegetable Growing (Almaty), employing 10 SSR markers associated with important agronomic traits. SSR genotyping unveiled polymorphisms across 6 markers with variable allele numbers. Genetic diversity metrics highlighted significant genetic diversity within both outdoor and greenhouse tomato cultivars and lines. Bayesian clustering, Neighbor-joining (NJ) clustering, and principal coordinate analysis (PCoA) delineated genetic differentiation between outdoor and greenhouse tomatoes with small admixture, indicating distinct breeding directions for these two types. Highly polymorphic SSRs (PIC &gt; 0.5) associated with essential fruit traits emerge as promising targets for marker-assisted selection (MAS) that can be used to enhance tomato breeding efficiency in Kazakhstan. According to 8 SSRs, 22 out of 30 outdoor accessions and 8 greenhouse tomato accessions were genetically uniform. This study offers comprehensive insights into the genetic diversity and population structure of tomato cultivars and lines in Kazakhstan, laying the foundation for informed breeding endeavors aimed at bolstering yield and resilience in tomato crops.

SSR‐based analysis of structural variation of the Russian population of Puccinia striiformis f. sp. tritici in 2019–2021

AbstractThe importance of monitoring and management of yellow rust, caused by Puccinia striiformis f. sp. tritici (Pst), has markedly increased in Russia over recent years because of intensifying negative effects of this destructive disease on wheat production. The Pst virulence survey was conducted in 2019–2021 in the European (North‐West, Volga, North Caucasus) and Asian (Siberia) parts of Russia, and the same 109 isolates have been genotyped here with 20 SSR markers. Fifty‐three multilocus genotypes (MLGs) were detected, seven of which occurred in two or more regions. The most frequent MLG was found in three European Pst collections (except Dagestan) and Siberia. SSR‐based variation within the regional collections was low because many MLGs were closely related. Nevertheless, each collection contained relatively different small genotype groups. No clear geographic structure of the Russian Pst population was observed because the five studied regional collections shared groups of similar genotypes. The most singular SSR genotype was identified in the North‐West collection, but genotypes of four invasive isolates belonging to the PstS2 temperature‐adapted aggressive strain did not considerably differ from others. The observed heterozygosity at all SSR loci exceeded the expected one in all regional Pst collections, which could imply asexual reproduction of the pathogen. Both the SSR and virulence analyses demonstrated similar patterns of relationships between the regional Pst collections, although the magnitude of differences between the collections was larger for virulence pathotypes. However, no significant association was established between the virulence pathotypes and SSR genotypes because multiple pathotypes had the same genotype and vice versa.

Wheat Stem Rust Surveillance Reveals Two New Races of Puccinia graminis f. sp. tritici in South Africa During 2016 to 2020.

Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is an important disease of wheat in South Africa (SA) and is primarily controlled using resistant cultivars. Understanding virulence diversity of Pgt is essential for successful breeding of resistant cultivars. Samples of infected wheat stems were collected across the major wheat-growing regions of SA from 2016 to 2020 to determine the pathogenic variability of Pgt isolates. Seven races were identified from 517 isolates pathotyped. The most frequently found races were 2SA104 (BPGSC + Sr9h,27,Kw) (35% frequency) and 2SA88 (TTKSF + Sr8b) (33%). Race 2SA42 (PTKSK + Sr8b), which was found in 2017, and 2SA5 (BFGSF + Sr9h), identified in 2017, are new races. The Ug99 variant race 2SA42 is similar in its virulence to 2SA107 (PTKST + Sr8b) except for avirulence to Sr24 and virulence to Sr8155B1. Race 2SA5 is closely related in its virulence to existing races that commonly infect triticale. Certain races showed limited geographical distribution. Races 2SA5, 2SA105, and 2SA108 were found only in the Western Cape, whereas 2SA107 and 2SA42 were detected only in the Free State province. The new and existing races were compared using microsatellite (SSR) marker analysis and their virulence on commercial cultivars was also determined. Seedling response of 113 wheat entries against the new races, using 2SA88, 2SA88+9h, 2SA106, and 2SA107 as controls, revealed 2SA107 as the most virulent (67 entries susceptible), followed by 2SA42 (64), 2SA106 (60), 2SA88+9h (59), 2SA88 (25), and 2SA5 (17). Thus, 2SA5 may not pose a significant threat to local wheat production. SSR genotyping revealed that 2SA5 is genetically distinct from all other SA Pgt races.

Comprehensive approach to replenishing the English walnut gene pool through the study of local seed populations in Krasnodar Region

promising genotypes in the areas where this species grows. The identification of the valuable breeding forms of English walnut among local seed populations facilitates the solution of breeding problems and replenishes the collections of genetic resources with valuable specimens. In this work, we aim to assess the prospects of using new forms to solve breeding problems by means of phenotypic evaluation and molecular genetic analysis. The search for promising forms was carried out in 2022–2023 on the territory of settlements in the different districts of Krasnodar Krai. Economically valuable traits were recorded according to the “Program and Procedure for the Studying the Varieties of Fruit, Berry, and Nut Crops.” In order to assess the level of genetic diversity in the sample of new, promising forms of English walnut, SSR genotyping was carried out using seven microsatellite DNA markers: WGA001, WGA376, WGA069, WGA276, WGA009, WGA202, WGA089. The heterogeneous group of varieties and elite breeding forms of the North Caucasus Federal Scientific Center of Horticulture, Viticulture, and Winemaking, representing the overall diversity of the collection, was also included in the studied sample. The comparison of the polymorphism level in the studied specimens for both individual markers and the entire sample of markers suggests a relatively high heterogeneity of the new, promising forms included in the study. The use of UPGMA, PCoA, and analysis in STRUCTURE software allowed genetic relationships to be established between the new, promising forms and specimens from the genetic collection of the North Caucasus Federal Scientific Center of Horticulture, Viticulture, and Winemaking. The new forms were found not to form a separate cluster and to generally have an intermediate position between the three genotype groups in the gene pool collection. For the new forms, the effect of the Central Asian geneplasm was established, which determines the presence of several valuable breeding traits. Given the data on the genetic diversity of new, promising forms of English walnut relative to the genetically contrasting sample of breeding forms from the collection of the North Caucasus Federal Scientific Center of Horticulture, Viticulture, and Winemaking, it is reasonable to involve new forms in breeding in order to enrich the local English walnut gene pool.

Evolution of the Genetic Structure of the Didymella tanaceti Population During Development of Succinate Dehydrogenase Inhibitor Resistance.

Emergence of pathogens with decreased sensitivity to succinate dehydrogenase inhibitor fungicides is a global agronomical issue. Analysis of Didymella tanaceti isolates (n = 173), which cause tan spot of pyrethrum (Tanacetum cinerariifolium), collected prior to (2004 to 2005) and after (2009, 2010, 2012, and 2014) the commercial implementation of boscalid in Tasmanian pyrethrum fields identified that insensitivity developed over time and has become widespread. To evaluate temporal change, isolates were characterized for frequency of mutations in the succinate dehydrogenase (Sdh) B, C, and D subunits associated with boscalid resistance, mating type, and SSR genotype. All isolates from 2004 and 2005 exhibited wild-type (WT) Sdh alleles. Seven known Sdh substitutions were identified in isolates collected from 2009 to 2014. In 2009, 60.7% had Sdh substitutions associated with boscalid resistance in D. tanaceti. The frequency of WT isolates decreased over time, with no WT isolates identified in 2014. The frequency of the SdhB-H277Y genotype increased from 10.7 to 77.8% between 2009 and 2014. Genotypic evidence suggested that a shift in the population structure occurred between 2005 and 2009, with decreases in gene diversity (uh; 0.51 to 0.34), genotypic evenness (E5; 0.96 to 0.67), genotypic diversity (G; 9.3 to 6.8), and allele frequencies. No evidence was obtained to support the rapid spread of Sdh genotypes by clonal expansion of the population. Thus, insensitivity to boscalid has developed and become widespread within a diverse population within 4 years of usage. These results suggest that D. tanaceti can disperse insensitivity through repeated frequent mutation, sexual recombination, or a combination of both.

Comprehensive agrobiological assessment and analysis of genetic relationships of promising walnut varieties of the Nikitsky Botanical Gardens.

Walnut is an important horticultural crop, the production of which ranks second among all nut crops. Despite the significant demand in the domestic market in Russia, the industrial production of walnut fruits in Russia is currently underdeveloped. At the same time, there is a need to update the assortment with new highly productive varieties adapted to local agro-climatic conditions and having high quality nuts that are competitive at the world level. An important issue for the successful implementation of breeding programs is a comprehensive study of the gene pool. In this regard, within the framework of the study, the task was to evaluate promising varieties from the collection of the walnut gene pool of the Nikitsky Botanical Gardens and analyze genetic relationships based on microsatellite genotyping. On the basis of the performed phenotypic assessment, the study sample, which included 31 varieties, was divided into several groups according to the main phenotypic traits, such as frost and drought resistance, the start of the growing season, the ripening period, the weight and type of flowering, the weight of the fruit, and the thickness of the endocarp. Varieties with economically valuable traits that can be recommended as promising as initial parental forms in breeding work for resistance to abiotic stress factors have been identified, as well as varieties with increased productivity and large fruit sizes. Based on the analysis of eight SSR markers (WGA001, WGA376, WGA069, WGA276, WGA009, WGA202, WGA089 and WGA054), an analysis of the level of genetic diversity was performed and genetic relationships were established in the studied sample of varieties. Six (for WGA089) to eleven (for WGA276) alleles per locus have been identified. A total of 70 alleles were identified for the eight DNA markers used, with an average value of 8.75. Analysis of SSR genotyping data using Bayesian analysis established the presence of two main groups of genotypes. Taking into account the fact that all the studied varieties are selections from local seed populations in different regions of the Crimean Peninsula, the revealed level of polymorphism may indirectly reflect the level of genetic diversity of the local walnut populations. Furthermore, the presence of two genetically distant groups indicates the presence of two independently formed pools of the autochthonous gene pool of the species Juglans regia L. on the Crimean Peninsula.

Host-associated genetic differentiation and origin of a recent host shift in the generalist parasitic weed Phelipanche ramosa.

Branched broomrape, Phelipanche ramosa (L.) Pomel, is a globally distributed parasitic weed of economic importance. In Europe, where it is native, it can infest several crops, notably tomato, tobacco, and hemp. In western France, it has recently adapted to a new host crop, oilseed rape, causing substantial damage. The aim of this study was to investigate the evolutionary relationships and genetic differentiation among P. ramosa populations infesting different hosts. We collected 1611 P. ramosa samples from 109 fields cultivated with six different crops (oilseed rape, tobacco, hemp, tomato, lentil, and celery) and distributed among six European countries. All samples were genotyped for ten microsatellite loci and a subset of samples was sequenced for two nuclear genes and two chloroplast genes. Genetic differentiation among populations was high (F ST = 0.807) and mainly driven by differentiation among different host crops, with no significant geographic structure. Genetic structure analysis identified up to seven biologically meaningful clusters that matched with host crops of origin. Reconstructed networks of sequence haplotypes and multilocus SSR genotypes showed a large genetic divergence between samples collected on oilseed rape and samples collected on other crops. The phylogeny inferred from DNA sequences placed samples collected from oilseed rape as a basal lineage. Approximate Bayesian Computations were used to compare different evolutionary scenarios of divergence among the three main genetic clusters, associated, respectively, with oilseed rape, tobacco, and hemp as host crops. The best-supported scenario indicated that P. ramosa infesting oilseed rape derived recently from an ancient, unknown lineage. Our results suggest that a more complete description of the genetic diversity of P. ramosa is still needed to uncover the likely source of the recent adaptation to oilseed rape and to anticipate future new host shifts.

Genetic Diversity of Apple Clonal Rootstocks from the Collection of the Michurinsk State Agrarian University Based on SSR Markers.

The Michurinsk State Agrarian University (Michurinsk SAU) is one of the leading centers for breeding apple clonal rootstocks. A diverse collection of apple rootstocks, founded in 1930s by V.I. Budagovsky, is maintained at the Michurinsk SAU. In the present study, 87 rootstocks from this collection were analyzed using 18 SSR markers to assess their genetic diversity and relatedness. The detected polymorphism level was rather high compared to the previous estimates of apple rootstock genetic variability. A total of 199 alleles were detected with an average of 11.1 alleles per locus. Among the detected alleles, 67 (33.67%) were rare and 43 (21.61%) were unique. The average PIC value was 0.73, and the expected and observed heterozygosity averaged 0.76 and 0.69, respectively. All the studied accessions except two could be identified with the used marker set. Cluster analysis revealed several groups according to the rootstocks' pedigrees and genetic origin. Furthermore, Structure analysis revealed two main groups of the studied rootstock accessions. No significant differentiation of the studied sample according to dwarfing ability was detected, while weak differentiation was detected according to leaf color. SSR genotyping data can be used for rootstock fingerprinting and pedigree verification and will facilitate collection management. In addition, data on the genetic diversity and structure of the studied collection may be useful for further development of the Michurinsk SAU rootstock breeding program.

Understanding the genotypic and phenotypic structure and impact of climate on Phytophthora nicotianae outbreaks on potato and tomato in the eastern US.

Samples from potato fields with late blight-like symptoms were collected from eastern North Carolina in 2017 and the causal agent was identified as Phytophthora nicotianae. We have identified P. nicotianae in potato and tomato from North Carolina, Virginia, Maryland, Pennsylvania, and New York. Ninety-two field samples were collected from 46 fields and characterized for mefenoxam sensitivity, mating type, and SSR genotype using microsatellites. Thirty two percent of isolates were the A1 mating type, while 53% were A2 mating type. In six cases, both A1 and A2 mating type were detected in the same field in the same year. All isolates tested were sensitive to mefenoxam. Two genetic groups were discerned based on STRUCTURE analysis: one included samples from North Carolina and Maryland, and one included samples from all five states. The data suggest two different sources of inoculum from the field sites sampled. Multiple haplotypes within a field and the detection of both mating types in close proximity suggests that P. nicotianae may be reproducing sexually in North Carolina. There was a decrease in the average number of days with weather suitable for late blight, from 2012-2016 to 2017-2021 in all of the NC counties where P. nicotianae was reported. Phytophthora nicotianae is more thermotolerant than P. infestans and grows at higher temperatures (25-35°C) than P. infestans (18-22°C). Late blight outbreaks have decreased in recent years and first reports of disease are later, suggesting that the thermotolerant P. nicotianae may cause more disease as temperatures rise due to climate change.

Genetic diversity and distinctiveness of Chilean Limachino tomato (Solanum lycopersicum L.) reveal an in situ conservation during the 20th century

Landraces constitute a valuable genetic pool of increased diversity that can be exploited for agriculture sustainability, food security, food quality, and future yield increments. It also contributes to understanding a species’ origin, domestication, population dynamics, and diversity. Chilean tomato germplasm characterization and documentation are scarce. To elucidate its potential and distinctiveness, we assessed the genetic variability between and within accessions of tomato landraces grown in Chile between 1938 and 2016, determining the relationships between them and with some European and US heirloom varieties. For this purpose, the tomato plants were characterized using 72 descriptors for vegetative and reproductive morphology. In addition, molecular diversity and the determination of genetic patterns between tomato accessions were made using highly informative SSR markers. Our results indicate that the genetic structure among evaluated accessions is associated with differences between the Chilean landraces grown to 1938 and cultivars grown in Europe and USA. The Chilean cluster presented a high variability. The Limachino tomato landrace is close to Marmande but distinguishable on phenotype and the molecular basis for its private alleles, being grown in the territory of Limache before 1960 until the present day. Accessions of pink beefsteak tomato grown in Chile to 2015 are distant to the rest of the tomato accessions on morphotype and close in SSR genotype to the materials grown in Chile in 1938, supporting the hypothesis of a pre-green revolution tomato diversification in Chilean territory. Chilean tomato populations may impact breeding programs due to higher variability in yield components. Our results are consistent with other researchers that have proposed Mesoamerica and the Andes Region as tomatoes’ primary center of diversity.

Seed Phenotyping and Genetic Diversity Assessment of Cowpea (V. unguiculata) Germplasm Collection

Cowpea is a nutrient-rich staple legume and climate-resilient crop for vulnerable agroecosystems. However, the crop still remains underutilized, mainly due to its narrow genetic base, and the production is often ravaged by aphid infestation outbreaks. Thus, genetic diversity assessment and the detection of defense-related alleles are fundamental to germplasm management and utilization in breeding strategies to support food safety in climate change times. A germplasm collection of 87 cowpea landraces sourced from Greece was subjected to seed phenotyping, SSR genotyping and to screening for the presence of aphid-resistance-conferring alleles. Significant diversity in the species’ local germplasm was revealed. The landraces were grouped in metapopulations based on their broader geographical origin. High amounts of variation and statistically significant differences were detected among the landraces regarding the seed morphological traits, the seed color and eye color according to MANOVA (Wilk’s λ = 0.2, p &lt; 0.01) and significant correlations were revealed among these features according to Pearson’s test (p &lt; 0.05). High levels of genetic polymorphism were detected for the metapopulations, ranging from 59% (VuPop3) to 82% (VuPop4). The AMOVA revealed that 93% of the molecular diversity was distributed among the landraces of each metapopulation. Further population structure analysis presumed the existence of two inferred populations, where in population A, 79% of the landraces have a cream/cream-brown seed coat, whereas in population B, 94% of the landraces are brown-ochre to black-seeded. Molecular screening for alleles conferring aphid resistance revealed the correspondence of 12 landraces to the resistant genotype of TVu-2876. The study highlights the importance of cowpea germplasm collection genetic diversity, as a source of important agronomic traits, to support breeding efforts and expand cowpea cultivation to foster food security and agriculture sustainability and diversification in climate change.

Genetic diversity analysis of apricots from Dagestan using SSR markers

Background. This publication presents the results of a study into the genetic structure of apricot genotypes from Dagestan using the SSR genotyping technique. The importance of the study is seen in the still underexplored gene pool of Dagestani apricot at the genetic level. With this in view, an assessment of the Dagestani apricot genetic diversity, followed by an analysis of its genetic structure, is of theoretical and practical interest.Materials and methods. The study included 27 apricot genotypes of Dagestani origin: 9 advanced contemporary cultivars and hybrids, 15 seed selections and landraces, and 3 wild forms. Eight SSR markers were used for the genetic diversity analysis: H1-3, A1-91, H2-79, H1-26-2, H2-16, A1-17, RPPG1-032, and RPPG3-026.Results. The UPGMA and NJ dendrogram construction techniques revealed the genetic similarity among the Dagestani apricots, confirmed by a low level of cluster significance. The tendency towards setting apart the genotypes of hybrid origin (obtained from free pollination of introduced cultivars) from the locally selected cultivars was observed by comparing the results of Bayesian analysis and the K-means approach using the Structure and Statistica software. Such isolation is partial, being obviously affected by constant integration of new apricot genotypes into the local gene pool and its enrichment with new alleles at the genetic level.Conclusion. The contemporary assortment of apricots in Dagestan was formed on the basis of both the local autochthonous gene pool and Central Asian and European cultivars introduced into this area. The obtained data will enrich the knowledge about the genetic diversity of apricots in Dagestan and serve as the platform for further studies into the florigenetic links of the North Caucasus with other regions.

Sui Generis Development of Molecular Markers from Transcriptome of Crotalaria juncea, a Fabaceae Family Bast Fiber Crop

ABSTRACT Lack of genomic resources in sunn hemp (Crotalaria juncea L.), a leguminous bast fiber crop, is one of the major constraints for germplasm characterization and genetic analysis. We identified non-redundant sets of a variety of molecular markers from the de novo flower-bud transcriptome of sunn hemp. These molecular markers included 1683 simple sequence repeats, 4759 intron length polymorphism markers primarily from protein-coding genes, and 3309 single nucleotide polymorphism allele-specific markers. All of these marker resources have been integrated into a simple database for easy access. To evaluate marker efficiency and polymorphism information content of the sampled primers, a subset of SSR and intron length polymorphism markers were validated in sunn hemp germplasm accessions to obtain average PIC values of 0.26–0.32. The SSR genotyping profiles also aided in the genetic distance matrix-based clustering of sunn hemp germplasm accessions. The ability of these molecular markers to successfully amplify in cross-genera bast fiber crops further demonstrated their effectiveness in genotyping. Thus, the current study describes the identification of previously undisclosed endogenous molecular markers in sunn hemp, which have potential applications in genetic studies and breeding in sunn hemp for bast fiber improvement.

Impact of inbreeding on growth and development of young open-pollinated progeny of Eucalyptus globulus

The use of open-pollinated seeds from seed orchards is a common strategy for the deployment of genetically improved eucalypts, including Eucalyptus globulus, an important pulpwood tree in many temperate climate areas. However, seed quality can be affected by the rate of selfing and to a lesser extent by contamination from pollen outside the orchard. Inbreeding between related parents and especially from self-crosses is known to cause diminished growth and developmental abnormalities in the resulting progeny. This study looks at the magnitude and variation in selfing and the impact in inbreeding depression across several E. globulus families collected over the years in a seed orchard. The effects on growth and development of outcrossed and selfed progeny were studied across five progeny trials, after pedigree reconstruction of the open pollinated progeny based on SSR genotyping. An additive genetic mixed linear model was fitted to the data to evaluate the impact of inbreeding on height growth. The results showed a significant inbreeding depression, with a height growth reduction of 15% in selfed progeny, when compared with crosses from unrelated parents. These inbreeding depression values varied among families, ranging between 7% and 24%, evidencing the importance of genetic background. Contamination rates were on average 10% suggesting long distance pollen dispersal was present. A small number of abnormal phenotypes (less than 10%) was observed in the field. This was associated with specific, unrelated, crosses and not to high inbreeding rates such as found among selfed progeny. The relevance of these results for orchard management and parent selection is discussed.

Assessment of Genetic Diversity for Cercospora Leaf Spot (CLS) Resistance in Mung Bean [Vigna radiata (L.) Wilczek] using SSR Markers

Background: CLS causes severe yield loss in mung bean. To sustain mung bean health, it is vital to include alleles that may be useful in resisting CLS. Therefore, in the present study, 90 mung bean genotypes were included for assessing genetic diversity using 66 SSR markers for CLS resistance. Methods: The mung bean crop was regularly monitored for the presence of pathogen and development of CLS disease in natural field conditions during pre rabi 2018 and pre rabi 2019. CLS screening assessments of germplasms were carried out using a 1-5 rating scale. Total genomic DNA was isolated from the leaf samples of all the genotypes and SSR genotyping was performed. The genotyping data were analysed by using GenAlEx 6.51b2 and TASSEL 5.0 software programme for genetic diversity parameters. Result: A moderate molecular diversity was observed in the panel population as a wide variation in alleles showed a range of 80 bp to 300 bp with the average PIC value of 0.40. The maximum percentage of polymorphic loci was 75.76% in the resistance genotypes followed by 56.06% in moderately resistant genotypes. The percentages of Shannon information among and within the population were found to be 44% and 56%, respectively. The archaeopterx tree differentiated the panel population into two major clusters, i.e., cluster I and cluster II, which were again sub divided into different sub-clusters and sub-sub clusters. These findings indicate that, the mung bean germplasm panel used in the present study could enrich the local gene pool and provide information for CLS resistance breeding.

Stripe rust and leaf rust resistance in CIMMYT wheat line “Mucuy” is conferred by combinations of race-specific and adult-plant resistance loci

Developing wheat varieties with durable resistance is a core objective of the International Maize and Wheat Improvement Center (CIMMYT) and many other breeding programs worldwide. The CIMMYT advanced wheat line “Mucuy” displayed high levels of resistance to stripe rust (YR) and leaf rust (LR) in field evaluations in Mexico and several other countries. To determine the genetic basis of YR and LR resistance, 138 F5 recombinant inbred lines (RILs) derived from the cross of Apav#1× Mucuy were phenotyped for YR responses from 2015 to 2020 at field sites in India, Kenya, and Mexico, and LR in Mexico. Seedling phenotyping for YR and LR responses was conducted in the greenhouse in Mexico using the same predominant races as in field trials. Using 12,681 polymorphic molecular markers from the DArT, SNP, and SSR genotyping platforms, we constructed genetic linkage maps and QTL analyses that detected seven YR and four LR resistance loci. Among these, a co-located YR/LR resistance loci was identified as Yr29/Lr46, and a seedling stripe rust resistance gene YrMu was mapped on the 2AS/2NS translocation. This fragment also conferred moderate adult plant resistance (APR) under all Mexican field environments and in one season in Kenya. Field trial phenotyping with Lr37-virulent Puccinia triticina races indicated the presence of an APR QTL accounting for 18.3–25.5% of the LR severity variation, in addition to a novel YR resistance QTL, QYr.cim-3DS, derived from Mucuy. We developed breeder-friendly KASP and indel molecular markers respectively for Yr29/Lr46 and YrMu. The current study validated the presence of known genes and identified new resistance loci, a QTL combination effect, and flanking markers to facilitate accelerated breeding for genetically complex, durable rust resistance.

Discerning the global phylogeographic distribution of Phyllosticta citricarpa by means of whole genome sequencing

Phyllosticta citricarpa is a fungal pathogen causing citrus black spot (CBS). As a regulated pest in some countries, the presence of the pathogen limits the export of fruit and is therefore of agricultural and economic importance. In this study, we used high throughput sequencing data to infer the global phylogeographic distribution of this pathogen, including 71 isolates from eight countries, Argentina, Australia, Brazil, China, Cuba, Eswatini, South Africa and the United States of America.We assembled draft genomes and used a pairwise read mapping approach for the detection and enumeration of variants between isolates. We performed SSR marker discovery based on the assembled genome with the best assembly statistics, and generated genotype profiles for all isolates with 1987 SSR markers in silico. Furthermore, we identified 32,560 SNPs relative to a reference sequence followed by population genetic analyses based on the three datasets; pairwise variant counts, SSR genotypes and SNP genotypes. All three analysis approaches gave similar overall results. Possible pathways of dissemination among the populations from China, Australia, southern Africa and the Americas are postulated. The Chinese population is the most diverse, and is genetically the furthest removed from all other populations, and is therefore considered the closest to the origin of the pathogen. Isolates from Australia, Eswatini and the South African province Mpumalanga are closely associated and clustered together with those from Argentina and Brazil. The Eastern Cape, North West, and KwaZulu-Natal populations in South Africa grouped in another cluster, while isolates from Limpopo are distributed between the two aforementioned clusters. Southern African populations showed a close relationship to populations in North America, and could be a possible source of P. citricarpa populations that are now found in North America.This study represents the largest whole genome sequencing survey of P. citricarpa to date and provides a more comprehensive assessment of the population genetic diversity and connectivity of P. citricarpa from different geographic origins. This information could further assist in a better understanding of the epidemiology of the CBS pathogen, its long-distance dispersal and dissemination pathways, and can be used to refine phytosanitary regulations and management programmes for the disease.

Genetic diversity and marker trait association for phytophthora resistance in chilli.

Chilli is an important commercial crop with positive returns tendency. Phytophthora root rot causes drastic damage to chilli plant. Dearth of detecting marker trait associations is a major hinderance in practicing marker assisted selection in chilli breeding. Herein, 110 chilli accessions were assessed for 15 agronomic traits under control and disease infected conditions for two crop seasons (2018-2019). The SSR genotyping revealed high values of major allele frequency (MAF = 0.70), genetic diversity (GD = 0.39) and Polymorphic Information Content (PIC = 0.31). Principal coordinate analysis and population structure analysis showed distribution of diverse genotypes in all groups by dividing 110 genotypes in three populations and nine sub-populations. The UPGMA based Archaeopteryx tree was in concordance with population structure analysis. Linkage disequilibrium analysis evaluated that LD decays within 3-10bp. Marker trait association (MTA) revealed the associations of 35 SSRs with 14 morphological traits. The significant MTA for marker CAeMS073 with relative leaf damage (RLD, 0.183 R2) under control and treated conditions was consistently observed in both models. The markers, CAMS173 and CAMS194 were found to be strongly associated with RLD and Disease Index (DI), respectively. The absence of MTA was detected for height of first branch. The MTAs reported in this study can facilitate marker assisted breeding for developing chilli germplasm resistant against Phytophthora capsici.