De Novo Transcriptome Assembly and SNP Discovery for the Development of dCAPS Markers in Oat

Cultivated oat (Avena sativa L.) is an important cereal crop that has captured interest worldwide due to its nutritional properties and associated health benefits. Despite this interest, oat has lagged behind other cereal crops in genome studies and the development of DNA markers due to its large and complex genome. RNA-Seq technology has been widely used for transcriptome analysis, functional gene study, and DNA marker development. In this study, we performed the transcriptome sequencing of 10 oat varieties at the seedling stage using the Illumina platform for the development of DNA markers. In total, 31,187,392~41,304,176 trimmed reads (an average of 34,322,925) were generated from 10 oat varieties. All of the trimmed reads of these varieties were assembled and generated, yielding a total of 128,244 assembled unigenes with an average length of 1071.7 bp and N50 of 1752 bp. According to gene ontology (GO) analysis, 30.7% of unigenes were assigned to the “catalytic activity” of the parent term in the molecular function category. Of the 1273 dCAPS markers developed using 491 genotype-specific SNPs, 30 markers exhibiting polymorphism in 28 oat varieties were finally selected. The transcriptome data of oat varieties could be used for functional studies about the seedling stage of oat and information about sequence variations in DNA marker development. These 30 dCAPS markers will be utilized for oat genetic analysis, cultivar identification, and breeders’ rights protection.

Molecular (ISSR, cp DNA, ITS) and Morphological Study of the Genus Tragopogon L. (Asteraceae)

Tragopogon L. (Cichorioideae, Lactuceae, Scorzonerinae) is an Old World genus with 150 species, Rechinger in Flora Iranica divided this genus in 13 section and 37 species that 26 species of them are exist in Iran. Safavi et al. divided it into 26 species without sections in flora Iran. Despite the anatomical and molecular studies done around the world, the exact classification of this genus is not clear due to the high number of secret species, hybridization, polyploidy and rapid diversification. The morphology studies of 32 species and Molecular studies (ISSR, ITS, cp DNA) of 22 species of the genus Tragopogon was investigated . The purpose of these studies are classification and determination of interspecific relationship in this genus. Sections of Rubriflori, Sosnowskya, Chromopappus, Majores, Angustissimi, Krascheninnikovia in flora of Iranica are confirmed on the basis of morphometry and molecular data. Section of Profundisulcati in flora Iranica is confirmed on the base of morphometry data. The Species of T. jesdianus, T . porphyrocephalus, T. rezaiyensis and T. Stroterocarpus in the flora of Iranica are not classified in any section which we classified in the Rubriflori section, Cp DNA dendrogram are not useful for classification in this genus and Chloroplast sequences are very similar among Tragopogon species, Therefore, the use of cp DNA markers in the classification of this genus is not recommended.

Novel DNA Markers for Identification of Actinobacillus pleuropneumoniae

Species-specific markers are crucial for infectious disease diagnostics. Mutations within a marker sequence can lead to false-negative results, inappropriate treatment, and economic loss.

Development of Disease-Resistance-Associated Microsatellite DNA Markers for Selective Breeding of Tilapia (Oreochromis spp.) Farmed in Taiwan

There are numerous means to improve the tilapia aquaculture industry, and one is to develop disease resistance through selective breeding using molecular markers. In this study, 11 disease-resistance-associated microsatellite markers including 3 markers linked to hamp2, 4 linked to hamp1, 1 linked to pgrn2, 2 linked to pgrn1, and 1 linked to piscidin 4 (TP4) genes were established for tilapia strains farmed in Taiwan after challenge with Streptococcus inae. The correlation analysis of genotypes and survival revealed a total of 55 genotypes related to survival by the chi-square and Z-test. Although fewer markers were found in B and N2 strains compared with A strain, they performed well in terms of disease resistance. It suggested that this may be due to the low potency of some genotypes and the combinatorial arrangement between them. Therefore, a predictive model was built by the genotypes of the parental generation and the mortality rate of different combinations was calculated. The results show the same trend of predicted mortality in the offspring of three new disease-resistant strains as in the challenge experiment. The present findings is a nonkilling method without requiring the selection by challenge with bacteria or viruses and might increase the possibility of utilization of selective breeding using SSR markers in farms.

Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton (Gossypium spp.)

Cotton genetic resources contain diverse economically important traits that can be used widely in breeding approaches to create of high-yielding elite cultivars with superior fiber quality and adapted to biotic and abiotic stresses. Nevertheless, the creation of new cultivars using conventional breeding methods is limited by the cost and proved to be time consuming process, also requires a space to make field observations and measurements. Decoding genomes of cotton species greatly facilitated generating large-scale high-throughput DNA markers and identification of QTLs that allows confirmation of candidate genes, and use them in marker-assisted selection (MAS)-based breeding programs. With the advances of quantitative trait loci (QTL) mapping and genome-wide-association study approaches, DNA markers associated with valuable traits significantly accelerate breeding processes by replacing the selection with a phenotype to the selection at the DNA or gene level. In this review, we discuss the evolution and genetic diversity of cotton Gossypium genus, molecular markers and their types, genetic mapping and QTL analysis, application, and perspectives of MAS-based approaches in cotton breeding.

POLYMORPHISM OF PROLACTIN AND SOMATOTROPIN GENES IN DAIRY CATTLE OF THE REPUBLIC OF TATARSTAN

Изучен полиморфизм и определена частота встречаемости аллельных вариантов по генам пролактина (PRL) и соматотропина (GH) у коров в условиях двух племенных хозяйств Республики Татарстан. Объектом исследования были животные черно-пестрой породы первого (n=151) и третьего (n=168) отелов и холмогорской породы первого (n=160) и третьего (n=143) отелов. Проведено генотипирование коров по генам PRL и GH методом ДНК-диагностики. Установлено, что среди молочного скота преимущественно встречаются особи с генотипом PRL АА (70,0—77,5%), с частотой аллеля А гена пролактина — 0,83—0,87, аллеля В — 0,13—0,17. Встречаемость аллеля В была выше среди холмогорских коров (0,16—0,17). В стаде полновозрастных животных черно-пестрой породы имеется сдвиг генетического равновесия в сторону генотипов PRL AA и PRL BB (χ2=3,97; Р<0,05). В исследуемых стадах крупного рогатого скота выражено преимущество генотипа GH LL с частотой встречаемости 51,0—79,2%. Встречаемость генотипа GH VV у черно-пестрого скота составила 2,0—2,4%, у холмогорского — 5,6—7,0%. Аллель L гена соматотропина преобладает над аллелем V в обеих породах. При этом чаще встречаемость аллеля L GH среди коров холмогорской породы (0,28—0,29). У холмогорских коров больше представлены редкие и желательные аллели генов PRL и GH. Чтобы повысить встречаемость «предпочтительных» в хозяйственном отношении генотипов и аллелей ДНК-маркеров, необходимо в большей степени использовать быков-производителей с желательными аллелями PRL и GH, а именно В и V соответственно. The polymorphism was studied and the frequency of occurrence of allelic variants for the genes of prolactin (PRL) and somatotropin (GH) was determinedin cows in two bred livestock farms of the Republic of Tatarstan. The object of the study were animals of the black-and-white breed of the first (n=151) and third (n=168) calving and the Kholmogory breed of the first (n=160) and third (n=143) calving. Genotyping of cows for PRL and GH genes was carried out using method of DNA diagnostics. It was revealed that there were mainly individuals with the PRL AA genotype (70,0–77,5%)among dairy cattle, the frequency of the A allele of the prolactin gene was 0,83–0,87, the B allele was 0,13–0,17. The frequency of allele B was higher among Kholmogory cows (0,16–0,17). There was a shift in the genetic balance towards the PRL AA and PRL BB genotypes (χ2=3,97; Р<0,05) in the herd of full-age animals of the black-and-white breed. The advantage of the GH LL genotype was expressed with a frequency of occurrence 51,0–79,2% in the studied cattle herds. The occurence of the GH VV genotype was 2,0–2,4%in black-and-white cattle, 5,6–7,0% was in Kholmogorycattle. The L allele of the somatotropin gene predominated over the V allele in both breeds. Moreover, the occurrence of the L GH allele among cows of the Kholmogory breed (0,28–0,29) was more often. Rare and desirable alleles of the PRL and GH genes are more represented in Kholmogory cows. In order to increase the occurrence of economically “preferred” genotypes and alleles of DNA markers, it is necessary to use more stud bulls with the desired PRL and GH alleles, namely B and V, respectively.

Molecular Dissection for Boll Shedding in Upland Cotton Using Microsatellites

DNA markers application in marker-assisted breeding of cotton is handicapped due to low genetic diversity in cotton germplasm. The present study was designed to identify DNA markers, predominately simple sequence repeats (SSRs), associated with tolerance/resistance to heat stress as a consequence of boll shedding. To find out the genetic diversity a total of 24 cotton genotypes and 50 SSR primers were used. Total 288 alleles were produced with an average of 5.7 alleles per primer. Bootstrap cluster analysis used to generate a dendrogram that cluster the 24 accessions into two main clusters. Eleven out of 24 genotypes fall in a single cluster. Phenotypically H-4074 gives more diversity, while genotypically H-4074 sheared the same genetic background as H-4070, H-4091 and H-4090. Low genetic diversity was observed among both genotypic and phenotypic as maximum varieties fall in single group. This study helps for selecting diverse accessions with multiple phenotypic traits, which were drought to boll shedding. It suggests further elaborating the molecular genetic diversity by using new SSR marker to improve the yield of cotton cultivars. These preliminary results set the stage for initiating in depth marker-trait association studies, which will be instrumental for initiating marker-assisted breeding in cotton.