The natural variation of starch phosphate content in potatoes has been previously reported. It is known that, in contrast to raw starch, commercially phosphorylated starch is more stable at high temperatures and shear rates and has higher water capacity. The genetic improvement of phosphate content in potato starch by selection or engineering would allow the production of phosphorylated starch in a natural, environmentally friendly way without chemicals. The aim of the current research is to identify genomic SNPs associated with starch phosphorylation by carrying out a genome-wide association study in potatoes. A total of 90 S. tuberosum L. varieties were used for phenotyping and genotyping. The phosphorus content of starch in 90 potato cultivars was measured and then statistically analysed. Principal component analysis (PCA) revealed that the third and eighth principal components appeared to be sensitive to variation in phosphorus content (p = 0.0005 and p = 0.002, respectively). PC3 showed the correlation of starch phosphorus content with allelic variations responsible for higher phosphorylation levels, found in four varieties. Similarly, PC8 indicated that hybrid 785/8–5 carried an allele associated with high phosphorus content, while the Impala and Red Scarlet varieties carried alleles for low phosphorus content. Genotyping was carried out using an Illumina 22 K SNP potato array. A total of 15,214 scorable SNPs (71.7% success rate) was revealed. GWAS mapping plots were obtained using TASSEL based on several statistical models, including general linear models (GLMs), with and without accounting for population structure, as well as MLM. A total of 17 significant SNPs was identified for phosphorus content in potato starch, 14 of which are assigned to 8 genomic regions on chromosomes 1, 4, 5, 7, 8, 10, and 11. Most of the SNPs identified belong to protein coding regions; however, their allelic variation was not associated with changes in protein structure or function. A total of 8 novel genomic regions possibly associated with starch phosphorylation on potato chromosomes 1, 4, 5, 7, 8, 10, and 11 was revealed. Further validation of the SNPs identified and the analysis of the surrounding genomic regions for candidate genes will allow better understanding of starch phosphorylation biochemistry. The most indicative SNPs may be useful for developing diagnostic markers to accelerate the breeding of potatoes with predetermined levels of starch phosphorylation.

Background: It is well-documented that (bio)chemical reaction capacity of raw potato starch depends on crystallinity, morphology and other chemical and physical properties of starch granules, and these properties are closely related to gene functions. Preparative yield, amylose/amylopectin content, and phosphorylation of potato tuber starch are starch-related traits studied at the genetic level. In this paper, we perform a genome-wide association study using a 22K SNP potato array to identify for the first time genomic regions associated with starch granule morphology and to increase number of known genome loci associated with potato starch yield.Methods: A set of 90 potato (Solanum tuberosumL.) varieties from the ICG “GenAgro” collection (Novosibirsk, Russia) was harvested, 90 samples of raw tuber starch were obtained, and DNA samples were isolated from the skin of the tubers. Morphology of potato tuber starch granules was evaluated by optical microscopy and subsequent computer image analysis. A set of 15,214 scorable SNPs was used for the genome-wide analysis. In total, 53 SNPs were found to be significantly associated with potato starch morphology traits (aspect ratio, roundness, circularity, and the first bicomponent) and starch yield-related traits.Results: A total of 53 novel SNPs was identified on potato chromosomes 1, 2, 4, 5, 6, 7, 9, 11 and 12; these SNPs are associated with tuber starch preparative yield and granule morphology. Eight SNPs are situated close to each other on the chromosome 1 and 19 SNPs—on the chromosome 2, forming two DNA regions—potential QTLs, regulating aspect ratio and roundness of the starch granules. Thirty-seven of 53 SNPs are located in protein-coding regions. There are indications that granule shape may depend on starch phosphorylation processes. TheGWDgene, which is known to regulate starch phosphorylation—dephosphorylation, participates in the regulation of a number of morphological traits, rather than one specific trait. Some significant SNPs are associated with membrane and plastid proteins, as well as DNA transcription and binding regulators. Other SNPs are related to low-molecular-weight metabolite synthesis, and may be associated with flavonoid biosynthesis and circadian rhythm-related metabolic processes. The preparative yield of tuber starch is a polygenic trait that is associated with a number of SNPs from various regions and chromosomes in the potato genome.

Peach (Prunus persica (L.)) is one of the major commercial stone fruit crops. A genetic analysis of peach collections around the world is essential for effective breeding programmes, and the development of genomic and marker-assisted selection. This study focuses on research on peach collection at the Nikita Botanical Garden and aims to identify single-nucleotide polymorphisms (SNPs) at the genome level and analyse the genetic diversity, population structure, and the linkage disequilibrium (LD) pattern among 161 cultivars and hybrids. A total of 288,784 SNPs were identified using the genotyping-by-sequencing (GBS) approach and, after filtering, 7803 high-quality SNPs were used in the analyses. The 161 accessions were clustered into two groups using principal component analyses (PCoA) and seven populations by ADMIXTURE v.1.3 software, which was confirmed using phylogenetic analyses. The distribution of the genotypes within subpopulations reflected any fruit-related traits. A low level of genetic diversity and medium linkage disequilibrium was detected in peach cultivars. The observed heterozygosity was lower than expected and varied from 0.11 to 0.22 in genotypes with different origins. Our results based on 7803 SNPs were compared with those based on 12 microsatellite markers and differences in clustering, observed heterozygosity, and phylogeny were identified. This highlights the need to analyse collections using whole-genome approaches.

Potato (Solanum tuberosum L.) is one of the most important food crops in the world. The genome of this potato species is autotetraploid and has a high level of heterozygosity, also this potato species is a cross-pollinated plant. These characteristics complicate the genetic analysis and breeding process. The tuber’s eye depth is an important trait that affects the suitability of potato varieties for processing. Potato breeding for this trait is based on phenotypic assessment. Identification of the loci that control tuber eye depth would allow diagnostic markers for the marker-assisted selection to be created. The aim of this study is to search for loci associated with the eye depth by analyzing Solanum tuberosum varieties from the GenAgro collection of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, genotyped using the Illumina 22K SNP potato array DNA chip. The 24 significant markers associated with the “eye depth” trait were identified using 15,214 SNP markers genotyped with the Illumina 22K SNP potato array chip and the general linear model (GLM) taking into account the population structure. Data obtained showed the presence of SNPs in four genomic regions: on chromosome 4 (1 marker in the 3.92 Mb area), 5 (1 marker in the 4.67 Mb area) and 10 (1 marker in the 4.87 Mb area and 21 markers in the region between 48.1–48.9 Mb). The results of localization in the region 48.1–48.9 Mb of chromosome 10 correspond to previously published studies, the remaining three regions were detected for the first time. DNA sections containing SNPs linked to the tuber’s eye depth were studied in the SolTub_3.0 potato genome assembly (https:// plants.ensembl.org/). KASP markers were developed based on the data obtained. It will be possible to screen the breeding material and to breed the varieties more effectively using current markers associated with a shallow tuber’s eye depth.

Starch is one of the most demanded renewable feedstock in the world. The degree of phosphorylation of native potato (Solanum tuberosum L.) starch is a practically important quantitative trait, significantly influencing its physical and chemical properties. In this study, we evaluated the genetic diversity of the population of potato varieties and quantified phosphorus content in potato tuber starch harvested in 2017, 2018, and 2019. With the statistical methods, the most promising varieties for the next generation of breeding were identified for the first time. Genotyping and chemotyping data were utilized for genome-wide associations study (GWAS) in order to reveal genetic factors underlying the trait. GWAS based on a general linear model (GLM) with principal component analysis (PCA) was performed. The approach allowed us to identify two new, and confirm two previously found, significant SNPs on chromosome 5 associated with phosphorus content in starch. A search for the protein products coded in the genome regions carrying the significant SNPs revealed a cluster of genes that code glycoside and protein kinases, thus forming an operon-like structure. The genetic markers can be used for marker-assisted selection or to be considered as potential targets for genome editing to improve the industrially important properties of potato native starch via “intravital modification”.

Soybean (Glycine max (L.) Merr.) is one of the most important grain legume crops whose production has been growing every year and by 2024 reached ca. 7 million tons. The objective of this review was to summarize the latest achievements in soybean breeding, including the use of high-throughput sequencing methods and genomic technologies. Soybean is one of the most studied plants. The studies of recent years showed the advantage of approaches based on the use of molecular genetic markers in breeding. The first version of the soybean genome sequence, the G. max genome “Williams 82”, was presented in 2010, and this event significantly accelerated the study and development of genetic research on the crop. The data obtained made it possible to develop resources aimed at both studying the functional organization of soybean genes and breeding new improved cultivars. The review summarizes the results of large-scale soybean sequencing projects, including pan-genome works. Methods used for high-resolution genetic mapping, such as the SNP array analysis and the GBS (genotyping-by-sequencing) technique, are described. Information is provided on soybean genes associated with valuable agronomic and breeding-oriented traits whose identification made it possible to single them out as targets for editing.