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DNA markers have broad applications, including marker-assisted selection (MAS) for breeding new cultivars. Currently, single nucleotide polymorphisms (SNPs) have become a preferred choice of markers for molecular geneticists and breeders. They offer many advantages, such as high abundance and coverage in the genome, codominant inheritance, locus specificity, and flexibility for high-throughput genotyping/detection formats, and they are relatively inexpensive. The availability of reference genome sequences enables precise identification of candidate genes and SNPs associated with a trait of interest through quantitative trait loci mapping and genome-wide association studies. Such SNPs can be converted into markers for their application in MAS in crop breeding programs. Cleaved amplified polymorphic sequence (CAPS) markers amplify short genomic sequences around the polymorphic endonuclease restriction site. This review provides insight into the recent advancements made in the development and application of CAPS markers in several horticultural plants. We discussed many new tools that aid faster and more accurate design of CAPS markers from the whole genome resequencing data. The developed CAPS markers offer immense application in germplasm screening and field trials, genomic loci mapping, identifying candidate genes, and MAS of important horticultural traits such as disease resistance, fruit quality and morphology, and genetic purity. [ABSTRACT FROM AUTHOR]

The objective of this study was to determine the genetic relationship between the oleic acid and protein content. The genotypes having high oleic acid and elevated protein (HOEP) content were crossed with five elite lines having normal oleic acid and average protein (NOAP) content. The selected accessions were grown at six environments in three different locations and phenotyped for protein, oil, and fatty acid components. The mean protein content of parents, HOEP, and NOAP lines was 34.6%, 38%, and 34.9%, respectively. The oleic acid concentration of parents, HOEP, and NOAP lines was 21.7%, 80.5%, and 20.8%, respectively. The HOEP plants carried both FAD2-1A (S117N) and FAD2-1B (P137R) mutant alleles contributing to the high oleic acid phenotype. Comparative genome analysis using whole-genome resequencing data identified six genes having single nucleotide polymorphism (SNP) significantly associated with the traits analyzed. A single SNP in the putative gene Glyma.10G275800 was associated with the elevated protein content, and palmitic, oleic, and linoleic acids. The genes from the marker intervals of previously identified QTL did not carry SNPs associated with protein content and fatty acid composition in the lines used in this study, indicating that all the genes except Glyma.10G278000 may be the new genes associated with the respective traits. Key words: soybean, high oleic acid, elevated protein content, comparative genome analysis, whole-genome resequencing. L'objectif de ce travail etait de determiner la relation genetique entre les teneurs en acide oleique et en proteines. Des genotypes a teneur elevee en acide oleique et en proteines (HOEP) ont ete croisees avec des lignees elites presentant une teneur normale en acide oleique et une teneur moyenne en proteines (NOAP). Les accessions choisies ont ete cultivees dans six environnements sur trois sites et caracterisees pour leur teneur en proteine, en huile et en acides gras. Les teneurs moyennes en proteines chez les parents, HOEP et NOAP etaient respectivement de 34,6 %, 38 % et 34,9 %. Les concentrations en acide oleique chez les parents, HOEP et NOAP etaient respectivement de 21,7 %, 80,5 % et 20,8 %. Les plantes HOEP portaient deux alleles mutants, FAD2-1A (S117N) et FAD2-1B (P137R), contribuant au phenotype de forte teneur en acide oleique. Une analyse genomique comparee au moyen de donnees de re-sequencage pangenomique a identifie six genes presentant des polymorphismes mono-nucleotidiques (SNP) qui etaient significativement associes aux caracteres etudies. Un unique SNP situe dans le gene predit Glyma.10G275800 etait associe avec une teneur elevee en proteines, ainsi qu'en acides palmitiques, oleiques et linoleiques. Les genes situes dans des intervalles delimites par des marqueurs ayant precedemment permis d'identifier des QTL ne portaient pas de SNP associes avec la teneur en proteines et la composition en acides gras, ce qui suggere que tous les genes autres que Glyma.10G275800 pourraient constituer de nouveaux genes associes avec les caracteres respectifs. [Traduit par la Redaction] Mots-cles : soja, teneur elevee en acide oleique, teneur elevee en proteines, analyse genomique comparee, re-sequencage pangenomique., Introduction Soybean (Glycine max (L.) Merr.) is an important leguminous crop, domesticated worldwide primarily for its high protein and oil content (Vuong et al. 2007). Soybean food products have become [...]

Blueberry (Vaccinium spp.) is one of the most economically important berry crops worldwide. Validation of genetic mapping studies is often hindered by asynchronous marker technology. The development of a standardized genotyping platform that targets a specific set of polymorphic loci can be a practical solution to unify the scientific and breeding community toward blueberry improvement. The objective of this study was to develop and evaluate a targeted genotyping platform for cultivated blueberries that is affordable, reproducible, and sufficiently high density to warrant large-scale adoption for genomic studies. The Flex-Seq platform was developed in a two-step procedure that resulted in 22,000 loci that yielded 194,365 single nucleotide polymorphisms when assessed in a diversity set of 192 samples including cultivated and other related wild Vaccinium species. Locus recovery averaged 89.4% in the cultivated polyploid blueberry (northern highbush [NHB], southern highbush [SHB], and rabbiteye [RE]) and on average 88.8% were polymorphic. While recovery of these loci was lower in the other Vacciniumspecies assayed, recovery remained high and ranged between 60.8% and 70.4% depending on the taxonomic distance to the cultivated blueberry targeted in this platform. NHB had the highest mean number of variants per locus at 9.7, followed by RE with 9.1, SHB with 8.5, and a range between 7.7 and 8.5 in other species. As expected, the total number of unique-instate haplotypes exceeded the total number of variants in the domesticated blueberries. Phylogenetic analysis using a subset of the SNPs and haplotypes mostly conformed to known relationships. The platform also offers flexibility about the number of loci, depth of sequencing for accurate dosage calling, loci and haplotype reconstruction from increased fragment length. This genotyping platform will accelerate the development and improvement of blueberry cultivars through genomic-assisted breeding tools. [ABSTRACT FROM AUTHOR]

Stearic acid is a relatively minor component of soybean [Glycine max (L.) Merr.] seed oil. Increasing the stearic acid concentration is desired for industrial and food applications, as well as enhanced oxidative stability of the oil. Several ethyl methane sulfonate (EMS)-induced mutants with elevated seed stearic acid concentration have been reported in soybean. Such mutants were often found to carry alterations in the GmSACPD-C gene encoding D9-stearoylacyl carrier protein-desaturase, the enzyme that catalyzes the conversion of stearic acid to oleic acid in the fatty acid biosynthetic pathway. In the present study, we identified a new GmSACPD-C allele in an EMS-induced high stearic-acid mutant PE980. The mutant showed a seed stearic acid concentration of ~160 g kg-1, fourfold that of the wild-type 'Pungsannamul'. A single base substitution from guanine to adenine at genomic position 703 of first exon of the GmSACPD-C gene was identified through sequencing, and validated by cosegregation analysis of 167 F2 plants using an allele-specific SimpleProbe marker. The mutation caused a valine to methionine (+70 position) change in the predicted GmSACPD-Cprotein sequence. The sequence alignments and three-dimensional structure modeling of GmSACPD-C showed that the V70M mutation affects substrate binding and dimerization to reduce enzyme activity. Since the mutant showed significant reductions in seed yield compared with the wild type, marker-assisted backcrossing may be needed to reduce the yield gap. [ABSTRACT FROM AUTHOR]

Blueberries (Vaccinium section Cyanococcus) are perennial shrubs widely cultivated for their edible fruits. In this study, we performed admixture and genetic relatedness analysis of northern highbush (NHB, primarily V. corymbosum) and southern highbush (SHB, V. corymbosum introgressed with V. darrowii, V. virgatum, or V. tenellum) blueberry genotypes, and progenies of the BNJ16-5 cross (V. corymbosum × V. darrowii). Using genotyping-by-sequencing (GBS), we generated more than 334 million reads (75 bp). The GBS reads were aligned to the V. corymbosum cv. Draper v1.0 reference genome sequence, and ~2.8 million reads were successfully mapped. From the alignments, we identified 2,244,039 single-nucleotide polymorphisms, which were used for principal component, haplotype, and admixture analysis. Principal component analysis revealed three main groups: (1) NHB cultivars, (2) SHB cultivars, and (3) BNJ16-5 progenies. The overall fixation index (FST) and nucleotide diversity for NHB and SHB cultivars indicated wide genetic differentiation, and haplotype analysis revealed that SHB cultivars are more genetically diverse than NHB cultivars. The admixture analysis identified a mixture of various lineages of parental genomic introgression. This study demonstrated the effectiveness of GBS-derived single-nucleotide polymorphism markers in genetic and admixture analyses to reveal genetic relatedness and to examine parental lineages in blueberry, which may be useful for future breeding plans. [ABSTRACT FROM AUTHOR]