Acca sellowiana, known as feijoa or pineapple guava, is a Myrtaceae fruit tree species native to Uruguay and Brazil. The species stand out for its highly aromatic fruits, with nutraceutical and therapeutic value. Despite its agronomically promising valuable, genetics studies on this species are limited. Linkage genetic maps are valuable tools for genetic and genomic studies, and can be employed in breeding programs to support the development of molecular breeding strategies. The lack of a high number of polymorphic markers is one of the main limitation to development saturated genetic maps. Recently, novel genotyping methods based on next generation sequencing technology allow to detect and genotype thousands of markers in mapping populations. This represents a rapid and cost-effective strategy, remarkably useful for minor species with limited genomic resources. In this study, we constructed a high-density integrated genetic linkage map of A. sellowiana using two populations, H5 (\'TCO × BR\' , n = 160) and H6 (\'TCO × DP\', n = 184), which have the same female parent. Genotyping by sequencing (GBS) approach was used to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in both populations. Two strategies were carried out to identify SNP markers: a reference pipeline using the reference genome of the closely-related species Eucalyptus grandis, and a de-novo pipeline that do not require a reference genome. After quantitative genotype calling, 5,350 and 4,227 high quality SNP markers were selected for mapping in H5 and H6 populations, respectively. The two resulting maps of populations H5 and H6 comprised 1,236 and 1,302 markers distributed over the expected 11 linkage groups. The H5 and H6 maps spanned a map length of 1,593 cM and 1,572 cM, with an average inter-marker distance of 1:29 cM and 1:21 cM, respectively. A high degree of collinearity was observed between the two maps. In addition, a large proportion of markers were common to both maps and were used to construct the composite genetic linkage map. A novel approach to estimate recombination of two connected populations is described, where the meiosis information of all individuals is captured in a single estimator using a multipoint maximum likelihood estimation. The composite map consisted of 641 SNPs markers with a total map length of 1011 cM. This composite map represent the best consensus ordering of markers, a valuable reference framework for future studies in A. sellowiana. The large number of SNPs identified allowed us to construct high-density genetic maps, molecular tools which represent a relevant contribution for future genetic research and breeding efforts in A. sellowiana. / Acca sellowiana, conhecida como feijoa, pineapple guava ou goiabeira-serrana, é uma árvore frutífera nativa do Uruguai e do Brasil, pertencente a família Myrtaceae. A espécie destaca-se por suas frutas altamente aromáticas, com reconhecido valor nutracêutico e terapêutico. Apesar do promissor valor agronômico, os estudos genéticos nesta espécie são limitados. Os mapas genéticos são valiosas ferramentas em tais estudos, sendo empregados no desenvolvimento de estratégias de melhoramento molecular nos programas de melhoramento. No entanto, a falta de um elevado número de marcadores polimórficos nas populações de mapeamento é uma das principais limitações no desenvolvimento de mapas genéticos saturados. Recentemente, novos métodos de genotipagem baseados em tecnologia de sequenciamento de nova geração permitem identificar e genotipar milhares de marcadores em populações de mapeamento. Esta rápida e eficiente estratégia é muito útil para culturas pouco estudadas, com recursos genômicos limitados. Neste estudo, foram construídos mapas genéticos saturados em A. sellowiana. Foram usadas duas populações de mapeamento, H5 (\'TCO × BR\', n = 160) e H6 (\'TCO × DP\', n = 184), conectadas geneticamente pelo mesmo genitor feminino. A estratégia de genotipagem por sequenciamento (genotyping by sequencing; GBS) foi usada para simultaneamente identificar e genotipar marcadores de polimorfismos de nucleotídeo único (single nucleotide polymorphism; SNP) em ambas populações. No processo de detecção de SNPs, duas estratégias foram implementadas: na primeira foi empregado o genoma de referência de especie relacionada Eucalyptus grandis; na segunda, foi empregado uma abordagem de novo, que não requer genoma de referência. Após o processo de genotipagem quantitativo, 5350 e 4227 SNPs de alta qualidade foram selecionados para mapeamento em H5 e H6, respectivamente. Os mapas integrados H5 e H6 compreendem 1236 e 1302 marcadores distribuídos no 11 grupos de ligação esperados. Os mapas genético abrangeram um comprimento total de 1593 cM e 1572 cM, com uma distância média entre marcadores de 1:29 cM e 1:21 cM, nas populações H5 e H6, respectivamente. Um alto nível de colinearidade foi observado entre os dois mapas. Além disso, uma grande proporção de marcadores foram mapeados em ambos mapas e posteriormente usados na construção de um mapa genético integrado, considerando a informação de ambas populações simultaneamente. Foi apresentada uma nova abordagem para estimar as frações de recombinação em duas populações conectadas, onde a informação das meioses de todos os indivíduos é capturado num único estimador, usando uma estimativa de máxima verossimilhança multiponto. O mapa integrado composto contém 641 marcadores SNP com um comprimento total de 1011 cM. Este mapa representa o melhor ordenamento consenso de marcadores, sendo una valiosa referencia para futuros estudos nesta espécie. O grande número de SNPs identificados permitiu-nos a construção de mapas genéticos de alta densidade, ferramentas moleculares que representam uma contribuição relevante para futuras pesquisas genéticas e avanços no melhoramento genético em A. sellowiana.

Cranberry common bean (Phaseolus vulgaris L.) is planted worldwide and consumed as a critical food source of human protein, fibre, carbohydrates, and minerals. Marsh spot (MS) is a physiogenic disorder which severely impacts seed quality in common beans. Previous studies indicate that MS involves a nutritional disorder caused by Mn deficiency. However, the inheritance and genetic mechanism of MS resistance are still not fully understood. To investigate the genetics of MS resistance, a population of 138 recombinant inbred lines (RILs) was developed from a bi-parental cross between a susceptible cultivar Messina and a resistant cultivar Cran09. The population and its two parents were evaluated for MS resistance during five consecutive years from 2015 to 2019 in both sandy and heavy clay soils in Morden, Manitoba, Canada. The severities of MS were rated and subsequently converted to MS resistance index (MSRI) and MS incidence (MSI). Statistical analyses indicated that MSI and MSRI were highly correlated (r = 0.96-0.99) and had high broad-sense heritability (H²) of 86.5% and 83.2%, respectively. Joint segregation analysis (JSA) of 18 phenotypic datasets from five years and two soil types showed that MS resistance was controlled by four major genes with genetic interactions - one of which may suppress the additive effect of the other three genes. To identify the quantitative trait loci (QTL) and the candidate genes associated with the MS resistance, the 138 RILs and the two parents were sequenced using genotyping by sequencing approach. A total of 52,676 SNPs were detected. After further filtering with a threshold of minor allele frequency > 0.01 and call rate > 20%, 2,061 SNPs were retained and then imputed for genetic map construction and QTL mapping. A genetic map consisting of 2,058 SNP markers on 11 linkage groups or chromosomes was constructed, which covered 1,004 recombination blocks with a total length of 6,449 cM and an average block of 6.42 cM. Three linkage map-based QTL-mapping models ICIM-ADD, ICIM-EPI, and GCIM and one genome-wide association study (GWAS) model RTM-GWAS for 18 phenotypic datasets from different years and soil types were used for identification of QTL. A total of 36 QTL, including 21 of additive and 15 of epistatic effects, were identified. Functional gene annotation analysis revealed 151 Mn-related candidate genes across the common bean reference genome and 17 of them harbored the six QTL discovered in this study. In conclusion, MS resistance in common bean is a highly heritable trait and controlled by several major and minor genes. The results of JSA and QTL mapping advance the current understanding of the genetic mechanisms of MS resistance in cranberry common bean, and provide additional resources for application in genomics-assisted breeding and potential isolation and functional characterization of the candidate genes.

The ability to identify germplasm and select traits accurately is fundamental to successful plant breeding. Pedigrees and molecular markers facilitate these processes; however misleading experimental results can occur when incorrect relationships and/or cultivar names are recorded. Molecular markers can identify these inconsistencies, and with advances in genotyping technology these diagnostics can be done faster and more objectively. This study aimed to develop molecular marker assays and graphical genotyping methodologies for cultivar identification, seed purity assessment and trait selection in oat (Avena sativa L.). KBioscience’s Allele-Specific PCR (KASP™) and genotyping-by-sequencing (GBS) technologies were applied to a set of current Canadian oat cultivars to evaluate their utility for identifying cultivars and detecting intra-cultivar variation. Both KASP™ and GBS detected different extents of heterogeneity among a set of 160 seeds that originated from four seed sources of four cultivars. In both cases, the detected variation did not appear to be limited to a specific cultivar or seed source, reinforcing that all cultivars are heterogeneous. Graphical genotyping localized heterogeneity to specific chromosome regions, thereby distinguishing physical contamination from true genetic heterogeneity and heterozygosity. Pre-existing genotype data for 700 oat cultivars and breeding lines were also used to construct graphical genotypes for pedigree validation and discovery of potential sources for favourable quantitative trait loci (QTL) alleles. This methodology used historical QTLs and anchoring markers to identify 25 putative “high oil” allele carriers. The results from this study will provide diagnostic tools for cultivar identification and pedigree validation, in addition to meaningful information about existing heterogeneity and possible QTL locations in current cultivars.

The ability to identify germplasm and select traits accurately is fundamental to successful plant breeding. Pedigrees and molecular markers facilitate these processes; however misleading experimental results can occur when incorrect relationships and/or cultivar names are recorded. Molecular markers can identify these inconsistencies, and with advances in genotyping technology these diagnostics can be done faster and more objectively. This study aimed to develop molecular marker assays and graphical genotyping methodologies for cultivar identification, seed purity assessment and trait selection in oat (Avena sativa L.). KBioscience’s Allele-Specific PCR (KASP™) and genotyping-by-sequencing (GBS) technologies were applied to a set of current Canadian oat cultivars to evaluate their utility for identifying cultivars and detecting intra-cultivar variation. Both KASP™ and GBS detected different extents of heterogeneity among a set of 160 seeds that originated from four seed sources of four cultivars. In both cases, the detected variation did not appear to be limited to a specific cultivar or seed source, reinforcing that all cultivars are heterogeneous. Graphical genotyping localized heterogeneity to specific chromosome regions, thereby distinguishing physical contamination from true genetic heterogeneity and heterozygosity. Pre-existing genotype data for 700 oat cultivars and breeding lines were also used to construct graphical genotypes for pedigree validation and discovery of potential sources for favourable quantitative trait loci (QTL) alleles. This methodology used historical QTLs and anchoring markers to identify 25 putative “high oil” allele carriers. The results from this study will provide diagnostic tools for cultivar identification and pedigree validation, in addition to meaningful information about existing heterogeneity and possible QTL locations in current cultivars.

Bermudagrass (Cynodon spp.) breeding and cultivar development is hampered by limited information regarding its genetic and phenotypic diversity. A germplasm collection of 206 bermudagrass accessions from 29 countries was genotyped with high-throughput genotyping-by-sequencing technique. Genomic diversity in this diverse germplasm panel was assessed with multifaceted approaches including population structure, phylogenetic analysis, principal component analysis, and genetic diversity parameters. This study revealed substantial genetic variation in the Cynodon accessions, demonstrating the potential of this germplasm panel for further genetic studies and cultivar development in breeding programs. Another critical issue in turfgrass breeding is the lack of information regarding the genetic architecture of traits. Four agronomic traits leaf length, leaf width, internode distance and stem diameter were evaluated in a germplasm panel of common bermudagrass accessions. Then genome-wide association study was performed to dissect the genetic basis of the traits.