Diagnostic DNA Markers Research Articles

Determination of genetic diversity of two Lessonia species from the Atacama region using ISSR markers

Lessonia nigrescens and L. trabeculata are economically important kelp species in northern Chile. Despite their considerable value, the genetic diversity of these kelp has received limited attention in the Atacama region. This study aimed to analyze genetic diversity, establish genetic relationships, and identify diagnostic DNA markers in the Atacama region's L. nigrescens and L. trabeculata. Both species' Inter-sequence simple repeat (ISSR) band patterns showed high reproducibility and reliability. Among 17 ISSRs, 161 polymorphic bands were identified in Lessonia spp. Parameters, such as percentage polymorphism, number of alleles per locus, effective number of alleles, and Shannon information index, indicated that L. nigrescens had slightly higher genetic diversity than L. trabeculata. The Unweighted pair group method with arithmetic average (UPGMA) cluster analysis revealed two main clusters: one containing L. nigrescens and the other containing L. trabeculata. Additionally, four species diagnostic ISSR markers were identified for L. nigrescens and L. trabeculata. The ISSR markers proved valuable in detecting genetic diversity in L. nigrescens and L. trabeculata. This information is particularly important for marine management strategies and ensuring successful conservation.

Study of a genetic collection of strawberry (Fragaria L.) for resistance to powdery mildew.

Powdery mildew (Sphaerotheca macularis Mag. (syn. Podosphaera aphanis Wallr.)) is a dangerous disease of strawberry (Fragaria L.). The resistance of strawberry to powdery mildew is controlled polygenically. Several genetic loci with a large contribution to disease resistance have been identified in various strawberry varieties. Diagnostic DNA markers have been developed for QTL 08 To-f. They showed a high level of reliable gene detection in mapping populations. The purpose of this study was assessment of a strawberry genetic collection for resistance to powdery mildew and identification of promising strawberry forms for breeding for resistance to S. macularis. The objects of the study were wild species of the genus Fragaria L., varieties and selected seedlings of strawberry (Fragaria × ananassa Duch.) created in the I.V. Michurin Federal Scientific Center, and strawberry varieties introduced from various ecological and geographical regions. To identify QTL 08 To-f, DNA markers IB535110 and IB533828 were used. Locus 08 To-f was detected in 23.2 % of the analyzed strawberry genotypes, including wild species F. moschata and F. orientalis, strawberry varieties of Russian breeding (Bylinnaya and Sudarushka) and foreign breeding (Florence, Korona, Malwina, Ostara, Polka and Red Gauntlet). The correlation between the presence of markers IB535110 and IB533828 and phenotypic resistance (powdery mildew effect on strawberry plants is absent) was 0.649. The determination coefficient (R2 ) showing the contribution of the studied locus to the manifestation of the trait was 0.421, that is, in 42.1 % of cases resistance was explained by the presence of QTL 08 To-f, and in 57.9 % of cases, by other genetic factors. All strawberry genotypes with locus 08 To-f were characterized by high field resistance to S. macularis in the conditions of Michurinsk, Tambov region. Thus, locus 08 To-f is promising for conferring resistance on local powdery mildew races, and markers IB535110 and IB533828 can be used in marker-assisted breeding programs to create powdery mildewresistant strawberry genotypes.

Identification of <i>Rca2</i> and <i>Rpf1</i> resistance alleles in strawberry breeding forms of intervarietal hybrid origin

Background. The creation of varieties with genetic resistance to fungal pathogens is one of the most important directions in strawberry breeding. A promising direction of accelerated selection of valuable specimens is molecular screening for the presence in their genotype of diagnostic DNA markers, linked to target genes of agrobiological traits. Objectives of the work were determination of the allelic state of the Rca2 (resistance to anthracnose) and Rpf1 (resistance to red stele root rot) genes in selected strawberry forms to identify genotypes resistant to Colletotrichum acutatum Simmonds and Phytophthora fragariae var. fragariae Hickman.Material and methods. The object of research was breeding forms of strawberries of intervarietal hybrid origin. As a result of 22 crossing combinations, 61 selection forms were obtained, in which the allelic composition of resistance genes was studied. The Rca2 anthracnose resistance allele was identified by means of the STS-Rca2_240 marker. The Rpf1 red stele root rot resistance allele was identified with the help of SCAR-R1A marker. Results. At least one of the two genes was identified in 20 selected strawberry forms (32.8%). The STS-Rca2_240 marker was identified in 15 strawberry seedlings (22.9%) from six hybrid combinations ‘Vicoda’ × ‘Roxana’, ‘Florence’ × ‘Faith’, ‘Asia’ × ‘Aprica’, ‘San Andreas’ × ‘Monterey’, ‘Alisa’ × ‘Quicky’, ‘Quicky’ × ‘Olympia’). The SCAR-R1A marker was identified in five strawberry seedlings (8.2%) from four hybrid combinations (‘Privlekatelnaya’ × ‘Bylinnaya’, ‘Feyerverk’ × ‘Bylinnaya’, ‘Bylinnaya’ × ‘Feyerverk’, ‘Bylinnaya’ × ‘Olimpiyskaya nadezhda’). It has been established that all strawberry selected forms with identified marker fragments for resistance genes are characterized by a heterozygous combination of alleles.Conclusions. Promising sources of resistance alleles are strawberry selected forms: 2/1-24, 2/1-34 (‘Quicky’ × ‘Olympia’), 3/9-5 (‘Florence’ × ‘Faith’), 3/12-2, 3/12- 9 (‘Alisa’ × ‘Quicky’), 4/7-10, 4/7-19, 4/7-20 (‘Asia’ × ‘Aprica’), 5/2-26, 5/2-32 (‘San Andreas’ × ‘Monterey’), 9/ 1-11, 9/1-12, 9/1-13, 9/1-32, 9/1-37 ‘Vicoda’ × ‘Roxana’) in case of Rca2 gene; 72-24, 72-71 (Privlekatelnaya × Bylinnaya), 69-29 (‘Feyerverk’ × ‘Bylinnaya’), 62-41 (‘Bylinnaya’ × ‘Feyerverk’), 61-15 (‘Bylinnaya’ × ‘Olimpiyskaya nadezhda’) in case of Rpf1 gene.

Registration of WGC002 spring wheat containing wild grass‐derived Fusarium head blight resistance gene Fhb7The2

AbstractThe USDA‐ARS and North Dakota State University Agricultural Experiment Station jointly released the Fusarium head blight (FHB)‐resistant spring wheat (Triticum aestivum L.) germplasm WGC002 (Reg. no. GP‐1089, PI 702949) in May 2023. WGC002 is a wheat‐Thinopyrum elongatum 7B‐7E translocation line, designated 7BS·7BL‐7EL, with the wheat chromosome 7BL terminal region replaced by the homoeologous counterpart of the Th. elongatum chromosome 7EL that contains the novel FHB resistance gene Fhb7The2. WGC002 was developed from the Chinese Spring (CS) wheat‐Th. elongatum disomic substitution line DS 7E(7B) using our genomics‐enabled chromosome engineering pipeline. The pedigree of WGC002 is DS 7E(7B)/2*CS ph1b mutant//DS 7E(7B). WGC002 has consistently exhibited resistance to FHB in inoculations of greenhouse grown plants. WGC002 does not contain the yellow flour pigment gene in the Fhb7The2 haplotype present on the terminal 7EL segment of the 7BS·7BL‐7EL translocation and has not exhibited any obvious linkage drag on the 7EL segment. Therefore, WGC002 is ready for immediate use in wheat breeding. One sequence‐tagged site (STS) and two polymerase chain reaction allelic competitive extension markers were developed specifically for Fhb7The2 and validated in different wheat genotypes. They are highly diagnostic for Fhb7The2 and extremely useful in marker‐assisted introgression of Fhb7The2 in wheat breeding. In summary, WGC002 is a new wild grass‐derived FHB‐resistant spring wheat germplasm with diagnostic DNA markers available to conduct marker‐assisted selection of Fhb7The2, that will enhance and diversify FHB resistance of wheat.

Genetic Dissection of Spike Productivity Traits in the Siberian Collection of Spring Barley.

Barley (Hordeum vulgare L.) is one of the most commonly cultivated cereals worldwide. Its local varieties can represent a valuable source of unique genetic variants useful for crop improvement. The aim of this study was to reveal loci contributing to spike productivity traits in Siberian spring barley and to develop diagnostic DNA markers for marker-assisted breeding programs. For this purpose we conducted a genome-wide association study using a panel of 94 barley varieties. In total, 64 SNPs significantly associated with productivity traits were revealed. Twenty-three SNP markers were validated by genotyping in an independent sample set using competitive allele-specific PCR (KASP). Finally, fourteen markers associated with spike productivity traits on chromosomes 2H, 4H and 5H can be suggested for use in breeding programs.

Cytogenetic and genomic characterization of a novel tall wheatgrass-derived Fhb7 allele integrated into wheat B genome.

We identified and integrated the novel FHB-resistant Fhb7The2 allele into wheat B genome and made it usable in both common and durum wheat breeding programs without yellow flour linkage drag. A novel tall wheatgrass-derived (Thinopyrum elongatum, genome EE) Fhb7 allele, designated Fhb7The2, was identified and integrated into the wheat B genome through a small 7B-7E translocation (7BS·7BL-7EL) involving the terminal regions of the long arms. Fhb7The2 conditions significant Type II resistance to Fusarium head blight (FHB) in wheat. Integration of Fhb7The2 into the wheat B genome makes this wild species-derived FHB resistance gene usable for breeding in both common and durum wheat. By contrast, other Fhb7 introgression lines involving wheat chromosome 7D can be utilized only in common wheat breeding programs, not in durum wheat. Additionally, we found that Fhb7The2 does not have the linkage drag of the yellow flour pigment gene that is tightly linked to the decaploid Th. ponticum-derived Fhb7 allele Fhb7Thp. This will further improve the utility of Fhb7The2 in wheat breeding. DNA sequence analysis identified 12 single nucleotide polymorphisms (SNPs) in Fhb7The2, Fhb7Thp, and another Th. elongatum-derived Fhb7 allele Fhb7The1, which led to seven amino acid conversions in Fhb7The2, Fhb7Thp, and Fhb7The1, respectively. However, no significant variation was observed in their predicted protein configuration as a glutathione transferase. Diagnostic DNA markers were developed specifically for Fhb7The2. The 7EL segment containing Fhb7The2 in the translocation chromosome 7BS·7BL-7EL exhibited a monogenic inheritance pattern in the wheat genetic background. This will enhance the efficacy of marker-assisted selection for Fhb7The2 introgression, pyramiding, and deployment in wheat germplasm and varieties.

Genetic diversity in wild species and cultivars of strawberry for the FanAAMT gene controlling fruit flavor volatiles

Background. An important consumer trait of strawberry fruits is their aroma. Methyl anthranilate makes a considerable contribution to the fruit flavor. The methyl anthranilate content in strawberry fruits is controlled by the FanAAMT (аnthranilic acid methyltransferase) gene. Identification of genetic determinants for this trait facilitates targeted selection of promising forms based on diagnostic DNA markers. The purpose of this study was to study the allelic diversity of the FanAAMT fruit flavor gene in wild strawberry species and strawberry cultivars for identification of promising genotypes.Materials and methods. The objects of this study were wild species of Fragaria L. as well as F. × anaschata Kantor. and F. × ananassa Duch. cultivars of different ecogeographic origin. The FanAAMT gene was identified with the dominant marker FanAAMT.Results and conclusion. In the analyzed collection of strawberry genotypes, the FanAAMT gene was identified in 36.4% of the forms, including the wild species F. vesca L., F. moschata Duch. and F. virginiana subsp. platypetala (Rydb.) Staudt, and cv. ‘Kupchikha’ (F. × anaschata). Among the analyzed F. × ananassa cultivars, the FanAAMT gene was found in 31.6% of the tested forms, specifically in 27.3% of the 22 Russian cultivars, and 37.5% of the analyzed foreign ones. Promising sources of high methyl anthranilate content in fruits were identified: wild spp. F. moschata, F. vesca, and F. virginiana subsp. platypetala; cv. ‘Kupchikha’ (F. × anaschata); Russian garden strawberry cvs. ‘Bylinnaya’, ‘Zenit’, ‘Lastochka’, ‘Neznakomka’, ‘Feyerverk’ and ‘Tsarskoselskaya’; and foreign garden strawberry cvs. ‘Karmen’, ‘Ostara’, ‘Samson’, ‘Symphony’, ‘Troubadour’ and ‘Vima Tarda’, in which the functional allele of the FanAAMT gene was found. In the remaining studied strawberry genotypes the marker FanAAMT was not detected, which presumably indicates that the FanAAMT gene is absent. cells (R9.4.1).

New Insight into Taxonomy of European Mountain Pines, Pinus mugo Complex, Based on Complete Chloroplast Genomes Sequencing.

The Pinus mugo complex is a large group of closely related mountain pines, which are an important component of the ecosystems of the most important mountain ranges, such as the Alps, Carpathians and Pyrenees. The phylogenetic relationships between taxa in this complex have been under discussion for many years. Despite the use of many different approaches, they still need to be clarified and supplemented with new data, especially those obtained with high-throughput methods. Therefore, in this study, the complete sequences of the chloroplast genomes of the three most recognized members of the Pinus mugo complex, i.e., Pinus mugo, Pinus rotundata and Pinus uncinata, were sequenced and analyzed to gain new insight into their phylogenetic relationships. Comparative analysis of their complete chloroplast genome sequences revealed several mutational hotspots potentially useful for the genetic identification of taxa from the Pinus mugo complex. Phylogenetic inference based on sixteen complete chloroplast genomes of different coniferous representatives showed that pines from the Pinus mugo complex form one distinct monophyletic group. The results obtained in this study provide new and valuable omics data for further research within the European mountain pine complex. They also indicate which regions may be useful in the search for diagnostic DNA markers for the members of Pinus mugo complex and set the baseline in the conservation of genetic resources of its endangered taxa.

No hybridization and marked interspecific differences in individual growth rate in mixed cultures of Manila clam (Ruditapes philippinarum) and grooved carpet-shell clam (R. decussatus)

The Manila clam (Ruditapes philippinarum) was introduced in Europe in the 1970's and in the following years it became naturalized. Interactions with the native species include hybridization with the grooved carpet-shell (GCS) clam (R. decussatus), which may have both useful and undesirable consequences. Here we report an attempt to produce hybrids in captivity by crossing 3 females and 4–5 males of each species in a two-step protocol that favored hybrid fertilizations. One-hundred animals were sampled at 15 months after fertilization, and scored for one morphological diagnostic trait (siphon fusion) and two diagnostic genetic DNA markers (ITS-2 and Fas-i1). No hybrids were detected, although the 0% hybridization rate has an associated 95% confidence interval of 3.3%. This result suggests that successful hybrid fertilization may be infrequent and/or the hybrid offspring may have very low survival rate. Abundant offspring of the two parental species were obtained and provided an unprecedented opportunity to study the innate differences in biological traits between the two species without the confounding influence of environmental variability. Individuals with ripe gonads were significantly less frequent in the Manila clam, suggesting an innate trend to earlier summer spawning in this species. Manila clam grew 20% faster than GCS clam and showed 80% heavier shells. However GCS clam showed almost twice as much variability in size as Manila clam, and some individuals of this species were as large as the largest Manila clams. The observed difference in growth variability may reflect a general loss of genetic variability in Manila clam during the introduction in Europe, although a random effect from using a small number of parents in the mixed cross cannot be discarded. Discrimination between these explanations, as well as determining more precisely the occurrence of hybridization in hatcheries by studying larger numbers of parents and offspring, may help improving clam aquaculture in Europe while preserving the genetic resources of the GCS clam.

Development of diagnostic markers for a wheat leaf rust resistance gene Lr42 using RNA-sequencing

Wheat leaf rust is a prevalent foliar disease in wheat worldwide. Growing resistant cultivars is an effective strategy to minimize the impact of leaf rust on yield and grain quality. Lr42 is a leaf rust resistance gene identified from Aegilops tauschii and is still effective against current predominant leaf rust races in the United States and many other countries. In this study, we developed diagnostic DNA markers for Lr42 using the sequence polymorphisms of a differentially expressed gene (TaRPM1) encoding a putative NB-ARC protein in the Lr42 candidate region identified by RNA-sequencing of two near-isogenic lines contrasting in Lr42 alleles. Markers were designed based on a deletion mutation and a single nucleotide polymorphism (SNP) in the gene. Haplotype analyses of the newly developed markers in the three diversity panels demonstrated that they are diagnostic for Lr42, and superior to previously used markers in selection accuracy. These markers have the advantages of low cost and easy assay, and they are suitable for marker-assisted selection in breeding programs with either high- or low-throughput marker screening facilities.

Vernalization (VRN) and Photoperiod (PPD) Genes in Spring Hexaploid Wheat Landraces

The heading time in wheat and some other cereals is mainly determined by the genetic system of VRN (vernalization response) and PPD (photoperiod response) genes. Using diagnostic DNA markers, we analyzed VRN-A1, VRN-B1, VRN-D1, and PPD-D1 allelic diversity in a set of landraces representing seven hexaploid spring wheat species from several regions of Eurasia. The determination of the spring growth habit was found to be variable: in 55.3% accessions, it was controlled monogenically by a VRN gene; in 30.3% accessions, by a combination of two VRN genes; and in 2.6% accessions, trigenically. The dominant Ppd-D1a allele was almost completely absent (only 2.6%) in the landraces, which suggests it being secondary to the recessive ppd-D1b allele as well as increase in its frequency during the recent “green revolution.” In species T. aestivum, Т. compactum, T. petropavlovskyi, and T. tibetanum, the Vrn-D1a frequency was shown to increase eastward with maximum concentration in the regions of Afghanistan, India, and China. In species with a compact ear (T. antiquorum, T. sphaerococcum, and Asian forms of Т. compactum), the spring growth habit is controlled by a single Vrn-B1a allele, which indicates their possible initial distribution in the same gene pool. The European and Asian T. spelta subspecies, despite the very fragmented distribution range, have the same Vrn-A1b and Vrn-B1c alleles, which genetically unites these subspecies. A common set of alleles of the VRN genes in landraces and modern cultivars have provided the adaptability of wheat to diverse environmental conditions during the long period of its cultivation. The newly detected DNA fragments in the first intron of VRN-D1 and PPD-D1 loci may mark new alleles and be of interest for further examination and use in breeding programs.

Polymorphism of wild species of р. Malus MILL. according to powdery mildew resistance genes

Powdery mildew (Podosphaera leucotricha (Ell. E tEv.) Salm.) – is one of the most widespread apple diseases in world. Identification of forms, carrying resistance genes, is an important stage in breeding programs aimed at obtaining powdery mildew resistant apple varieties. Diagnostic DNA markers of target genes will increase reliability of identification and efficiency of apple breeding for the creation of resistant genotypes. The purpose of this study was molecular genetic testing of wild species of genus Malus Mill. According to Pl-1, Pl-w and Pl-d powdery mildew resistance genes for revealing polymorphism of the studied loci and identification of valuable genotypes for breeding. The study subjects were the wild species of genus Malus Mill. of different ecological and geographic origin. The Pl-1 gene was identified using AT20-SCAR marker, Pl-w gene - EM M02 marker, Pl-d gene - EM DM01 marker. AT20-SCAR marker (Pl-1 gene) was identified in 37.3 % of genotypes. EM M02 marker (Pl-w gene) was detected in 16.4 % of the studied forms. EM DM01 marker (Pl-d gene) is present in 10.4 % of the analyzed forms. At least one of the studied molecular markers is present in the genome of 52.2 % of apple wild species. The Pl-1 gene in apple wild species is most spread in Baccatae series, the Pl-w gene - in Baccatae and Sieboldinae series, the Pl-d gene - in Orientalis series. Wild species M. baccata 2319, M. mandshurica 41947, M. sachalinensis 85, M. sachalinensis 97, M. purpurea v. pendula 2396 are characterized by combination of Pl-1 and Pl-w genes; M. turkmenorum 13283 and M. turkmenorum 29 421 - Pl-1 and Pl-d genes; M. denticulata 29416 - Pl-w and Pl-d genes, which allows to recommend them as promising complex sources of high powdery mildew resistance for breeding.

Marker controlled screening of resistant to red stele root rot (Rpf1 gene) strawberry selected forms

The results of the analysis of allelic polymorphism of the Rpf1 red stele root rot resistance gene in strawberry hybrid forms using diagnostic DNA markers were shown. The recessive homozygous genotype (rpf1rpf1) was identified in strawberry seedlings 932-29 (F. virginiana subsp. platypetala (Rydb.) Staudt × Feyerverk), 933-4 (F. virginiana subsp. platypetala (Rydb.) Staudt × Rubinovyy kulon), 62-7, 62-23 (Bylinnaya × Feyerverk), 65-2, 65-15 (Olimpiyskaya nadezhda × Bylinnaya) and 35-16 (922-67 × Maryshka). The heterozygous state of the Rpf1 gene was identified in strawberry forms 69-29 (Feyerverk × Bylinnaya), 62-41 (Bylinnaya × Feyerverk), 72-24, 72-71 (Privlekatelnaya × Bylinnaya), 65-17, 65-24 (Olimpiyskaya nadezhda × Bylinnaya), which allows them to be used in breeding for resistance to P. fragariae var. fragariae as valuable initial forms.

Marker-assisted screening of promising forms in the strawberry breeding

The results of the use diagnostic DNA-markers in the breeding of strawberry (Fragaria × ananassa Duch.) were shown. The carriers of target alleles of red stele root rot resistance (F. virginiana Duch. ssp. platypetala, Bylinnaya, 69-29 (Feyerverk × Bylinnaya), 72-24 and 72-71 (Privlekatelnaya × Bylinnaya)), anthracnose resistance (Borovitskaya, Sudarushka, Elianny, Troubadour, 933-4 (F. virginiana Duch. ssp. platypetala × Rubinovyy kulon)), high mesifurane content in fruits (F. orientalis Los., F. moschata Duch., F. virginiana Duch. ssp platypetala, Lastochka, Torpeda, Flora, Samson, 932-29 (F. virginiana Duch. ssp. platypetala × Feyerverk), 56-5 (Gigantella × Privlekatelnaya)) and γ-decalactone content in fruits (F. orientalis Los., F. moschata Duch., F. ovalis Rydb., Bylinnaya, Kupchikha, Sonata, Vima Tarda) were identified. These genotypes are valuable initial forms for involvement in the breeding process to improve the strawberry assortment.

The In-Silico Development of DNA Markers for Breeding of Spring Barley Varieties That Are Resistant to Spot Blotch in Russia

The fungal pathogen Cochliobolus sativus Drechs. Ex Dastur, anamorph Bipolaris sorokiniana (Sacc.) Shoemaker is one of the most common barley pathogens worldwide and causes spot blotch and root rot in barley. Spot blotch is considered to be the major biotic stress hampering the commercial production of barley. During high disease severity, which occurs in the northwestern region of Russia once every three to four years, yield losses for barley may reach 40%. An increase in common root rot severity results in yield losses that can reach 80%. The goal of the current study was to identify significant markers that can be employed as diagnostic DNA markers to breed C. sativus pathogen-resistant varieties of barley. In 94 spring barley cultivars and lines, the resistance of seedlings and adult plants to the impact of C. sativus on their leaves and roots was investigated. Five genomic regions associated with resistance to Spot blotch were identified (on chromosome 1H (50–61.2 cM), 2H (68.7–69.68 cM), 3H (18.72–26.18 cM), 7H (7.52–15.44 cM)). No significant loci were determined to be associated with root rot. According to obtained data, 11 significant SNPs were converted into KASP markers and 6 markers located on chromosome 3H were determined to possess good accuracy and the potential to be employed in marker-assisted selection.

Analysis of polymorphism of strawberry genotypes (Fragaria L.) according to the strawberry red root spot resistance gene RPF1 for identification of strawberry forms promising for breeding and horticulture

Red root spot (Phytophthora fragariae var. fragariae Hickman) is one of the most important strawberry diseases in the temperate climate zone. Identification of forms, carrying resistance genes, is an important stage in breeding programs aimed at obtaining red root spot resistant strawberry varieties. Diagnostic DNA markers of target genes will increase reliability of identification and efficiency of strawberry breeding for the creation of resistant genotypes. The purpose of this study is analysis of polymorphism of wild species of Fragaria L. genus and strawberry varieties (F. × ananassa Duch.) according to the strawberry red root spot resistance gene Rpf1 using molecular markers. The research sunjects were the wild species F. orientalis Los., F. moschata Duch., F. ovalis Rydb., F. virginiana Duch. ssp. platypetala and strawberry varieties (F. × ananassa Duch.) of different ecological and geographic origin. Total genomic DNA of strawberry was extracted from the fresh leaves using the Puchooa method. To assess the allelic state of Rpf1 gene, SCAR-R1A marker (linked to the Rpf1 dominant allele) and OPO-16C marker (linked to the rpf1 recessive allele) have been used. SCAR-R1A marker was identified in wild species F. virginiana Duch. ssp. platypetala (vegetation region: British Columbia, Canada), pineapple strawberry varieties Bylinnaya and promising selected forms 62-41 (Bylinnaya × Feyyerverk), 65-17 and 65-24 (Olimpiyskaya nadezhda × Bylinnaya). These genotypes are characterized by heterozygous Rpf1rpf1 genotype according to Rpf1 gene (both markers are present in genotype) and can be used as red root spot resistance source in marker-assisted selection. In the remaining studied genotypes of strawberry, SCAR-R1A marker was not detected, which presumably indicated their homozygous recessive genotype rpf1rpf1 according to Rpf1 gene. The research results can be useful for breeders of strawberry and researchers of plant biodiversity of p. Fragaria.

ALLELIC DIVERSITY OF GENES CONTROLLING RESPONSES TO VERNALIZATION AND PHOTOPERIOD AMONG SPRING BREAD WHEAT VARIETIES OF DIVERSE GEOGRAPHIC ORIGIN

Spring bread wheat is the most important cereal crop, cultivated under various climatic conditions and on different latitudes. Modern molecular genetic studies of wheat are aimed at investigating the crop’s genetic potential. By now, molecular markers have been developed to identify alleles of the Vrn (vernalization response) and Ppd (photoperiod response) genes. Vrn genes are responsible for crop development rate regulation and crop yield structure. Ppd genes determine the response of plants to the length of the day, that is, the timing of flowering and the beginning of heading in plants under different cultivation conditions. The use of diagnostic DNA markers made it possible to analyze the presence of allelic combinations of the Vrn and Ppd genes in local and commercial wheat varieties from Europe, Asia, North and South Americas, Africa and Australia. This review summarizes the results of studies on the distribution of alleles of Vrn and Ppd genes in wheat breeding material over different geographical areas of its cultivation. For example, the dominant Vrn-A1a allele was found in 62% of European varieties; 52% of the studied Turkish wheat varieties carried dominant Vrn-B1 alleles. A dominant Vrn-D1 was found in 61% of Pakistani wheat accessions. Vrn-D1 is present in 41.9% of the studied varieties of Chinese wheat. Higher incidence of Ppd-D1A is typical for West European varieties. A Ppd-D1a allele was found in 58.6% of varieties preserved in the Turkish wheat collection, with a 60% frequency of this allele in commercial cultivars. Among local Afghan varieties, 97% are sensitive to photoperiod (carriers of Ppd-D1b); they are distributed throughout the country without much dependence on agroecological zones. All Pakistani varieties are insensitive to photoperiod (carriers of Ppd-D1a). In China, the highest incidence of the Ppd-D1a allele was observed in zone VII (87.5% of varieties).

Molecular Dissection of Quantitative Variation in Bermudagrass Hybrids (Cynodon dactylon x transvaalensis): Morphological Traits.

Bermudagrass (Cynodon (L.)) is the most important warm-season grass grown for forage or turf. It shows extensive variation in morphological characteristics and growth attributes, but the genetic basis of this variation is little understood. Detection and tagging of quantitative trait loci (QTL) affecting above-ground morphology with diagnostic DNA markers would provide a foundation for genetic and molecular breeding applications in bermudagrass. Here, we report early findings regarding genetic architecture of foliage (canopy height, HT), stolon (stolon internode length, ILEN and length of the longest stolon LLS), and leaf traits (leaf blade length, LLEN and leaf blade width, LW) in 110 F1 individuals derived from a cross between Cynodon dactylon (T89) and C. transvaalensis (T574). Separate and joint environment analyses were performed on trait data collected across two to five environments (locations, and/or years, or time), finding significant differences (P < 0.001) among the hybrid progeny for all traits. Analysis of marker-trait associations detected 74 QTL and 135 epistatic interactions. Composite interval mapping (CIM) and mixed-model CIM (MCIM) identified 32 main effect QTL (M-QTL) and 13 interacting QTL (int-QTL). Colocalization of QTL for plant morphology partially explained significant correlations among traits. M-QTL qILEN-3-2 (for ILEN; R2 = 11–19%), qLLS-7-1 (for LLS; R2 = 13–27%), qLEN-1-1 (for LLEN; R2 = 10–11%), and qLW-3-2 (for LW; R2 = 10–12%) were ‘stable’ across multiple environments, representing candidates for fine mapping and applied breeding applications. QTL correspondence between bermudagrass and divergent grass lineages suggests opportunities to accelerate progress by predictive breeding of bermudagrass.

Cluster oligonucleotide signatures for rapid identification by sequencing

BackgroundOligonucleotide signatures (signatures) have been widely used for studying microbial diversity and function in wet-lab settings, but using them for accurate in silico identification of organisms from high-throughput sequencing (HTS) data is only a proof of concept. Existing signature design programs for sequence signatures (signatures matching exactly one sequence) or clade signatures (signatures matching every sequence in a phylogenetic clade) are not able to identify all possible polymorphic sites for sequences with high similarity and perform poorly when handling large genome sequencing datasets.ResultsWe introduce cluster signatures: subsequences that match perfectly and exclusively any group of sequences in a data set. Cluster signatures provide complete recall for primer/probe design and increased discrimination between sequences beyond that of clade signatures. Using cluster signatures for in silico identification of HTS targets achieves good precision/recall and running time performance. This method has been implemented into an open source tool, the Automated Oligonucleotide Design Pipeline (adop), included in supplementary material and available at: https://bitbucket.org/wenchen_aafc/aodp_v2.0_release.ConclusionsCluster signatures provide a rapid and universal analysis tool to identify all possible short diagnostic DNA markers and variants from any DNA sequencing dataset. They are particularly useful in discriminating genetic material from closely related organisms and in detecting deleterious mutations in highly or perfectly conserved genomic sites.

Development and validation of diagnostic markers for Fhb1 region, a major QTL for Fusarium head blight resistance in wheat.

Functional markers were developed based on the critical sequence deletion of TaHRC in the Fhb1 region and validated to be diagnostic in a worldwide wheat collection. Wheat Fusarium head blight (FHB) is a devastating disease in wheat and barley worldwide. Growing FHB-resistant cultivars is an effective strategy to minimize FHB damage in wheat production. Fhb1 is a quantitative trait locus for FHB resistance with the largest effect on disease severity identified to date. With this study, we developed diagnostic DNA markers for Fhb1 by comparing the genomic sequences in Fhb1 region between near-isogenic lines contrasting in Fhb1 alleles and phenotypic effects of the markers. Two markers were developed based on a deletion mutation in an gene encoding a putative histidine-rich calcium-binding protein (TaHRC) and validated in different types of populations. Haplotype or sequence analyses of the two markers in the three sets of diversity panels demonstrated that they are diagnostic for Fhb1, and superior to all previously used markers in selection accuracy. They also have the advantages of low cost, easy assay, and are suitable for breeding programs with either high- or low-throughput marker laboratories.