Identification of Genetic Loci on Chromosome 4B for Improving the Grain Number per Spike in Pre-Breeding Lines of Wheat

The grain number per spike (GNPS) is an important yield component, and much attention is given to the increase in GNPS for current yield improvement of common wheat. Here, a panel of 259 pre-breeding lines and elite commercial varieties were collected for the investigation of 12 agronomic traits, especially for spike-related traits, with 2-year replicates. The high correlation between GNPS and kernel number per spikelet (KNS) suggested that the high GNPS trait in our pre-breeding lines was mainly controlled by grain set number per spikelet. Genome-wide association studies (GWAS) using the 660K SNP genotyping assay suggested that a major locus on chromosomes 4BS contributed to the high GNPS trait, which contributed to 33% and 48% of the variation in KNS and GNPS, respectively. A good diagnostic KASP marker AX-109286577 flanking the 4BS locus was developed for easy selection of the large spike trait. Taken together, the results suggested that untapped rare allele variation in our pre-breeding lines can be used for improvement of the yield component of set grain number per spike.

Genetic variation of CAST gene in Local Karnobat and Karnobat merino sheep breeds

Karnobat sheep plays an important role in the development of sheep breeding in Southeastern region of Bulgaria. They are valuable source of genetic material. The aim of present experiment was to determine the allele variation of CAST gene in Local Karnobat and Karnobat Merino sheep breeds. A total of 60 blood samples were collected – 30 per breed. DNA was extracted and genotypes of all animals were identified by means of PCR-RFLP technique. The restriction reactions were accomplished by specific enzyme MspI. As expected both breeds were characterized with low level of genetic diversity due to the fact that mostly maintaining selection has been implemented. In Local Karnobat sheep breed was identified only one heterozygous individual from all 30. In Karnobat merino were identified allele M with frequency 0,97 and allele N with frequency 0,03. Genotypes MM and MN were revealed with frequencies 0,93 and 0,07, respectively. According to the statistical analysis both breeds were in HWE equilibrium.

Comparative analysis of allele variation using allele frequencies according to sample size in Korean population

Background Allele frequency using short tandem repeats (STRs) is used to calculate likelihood ratio for database match, to interpret DNA mixture and to estimate ethnic groups in forensic genetics. In Korea, three population studies for 23 STR loci have been conducted with different sample size for forensic purposes. Objective We performed comparative analysis to determine how the difference of sample size affects the allele frequency and allele variation within same ethnic population (i.e. Korean). Furthermore, this study was conducted to check how the sampling group and multiplex kit also affect allele variation such as rare alleles and population specific alleles. Methods To compare allele variation, we used allele frequencies of three population data published from three Korean forensic research groups. Allele frequencies were calculated using different sample sizes and multiplex kits: 526, 1000, and 2000 individuals, respectively. Results The results showed the different distribution of allele frequencies in some loci. There was also a difference in the number of rare alleles observed by the sample size and sampling bias. In particular, an allele of 9.1 in the D2S441 locus was not observed in population study with 526 individuals due to multiplex kits. Conclusion Because the allele frequencies play an important role in forensic genetics, even if the samples are derived from the same population, it is important to consider the effects of sample size, sampling bias, and selection of multiplex kits in population studies.

Application of the random forest algorithm to Streptococcus pyogenes response regulator allele variation: from machine learning to evolutionary models

Group A Streptococcus (GAS) is a globally significant bacterial pathogen. The GAS genotyping gold standard characterises the nucleotide variation of emm, which encodes a surface-exposed protein that is recombinogenic and under immune-based selection pressure. Within a supervised learning methodology, we tested three random forest (RF) algorithms (Guided, Ordinary, and Regularized) and 53 GAS response regulator (RR) allele types to infer six genomic traits (emm-type, emm-subtype, tissue and country of sample, clinical outcomes, and isolate invasiveness). The Guided, Ordinary, and Regularized RF classifiers inferred the emm-type with accuracies of 96.7%, 95.7%, and 95.2%, using ten, three, and four RR alleles in the feature set, respectively. Notably, we inferred the emm-type with 93.7% accuracy using only mga2 and lrp. We demonstrated a utility for inferring emm-subtype (89.9%), country (88.6%), invasiveness (84.7%), but not clinical (56.9%), or tissue (56.4%), which is consistent with the complexity of GAS pathophysiology. We identified a novel cell wall-spanning domain (SF5), and proposed evolutionary pathways depicting the ‘contrariwise’ and ‘likewise’ chimeric deletion-fusion of emm and enn. We identified an intermediate strain, which provides evidence of the time-dependent excision of mga regulon genes. Overall, our workflow advances the understanding of the GAS mga regulon and its plasticity.

Canine DVL2 variant contributes to brachycephalic phenotype and caudal vertebral anomalies

A frameshift deletion variant in the Wnt pathway gene dishevelled 2 (DVL2) is associated with a truncated, kinked tail (“screw tail”) in English Bulldogs, French Bulldogs and Boston Terriers. These breeds are also characterized by distinctive morphological traits, including a wide head, flat face and short-limbed dwarfism, which are characteristic of Robinow syndrome in humans, caused by defects in genes such as DVL1 and DVL3. Based on these phenotypic and genetic similarities, it has previously been hypothesized that the canine DVL2 variant results in a syndromic phenotype called the Robinow-like syndrome. In our study, we investigated the distribution of the DVL2 variant in 1954 dogs from 15 breeds, identifying breeds with allele variation and enabling the dissection of the genotype–phenotype correlation for the first time. With CT examinations in American Staffordshire Terriers, we confirmed that the DVL2 allele is associated with caudal vertebral malformations and a brachycephalic phenotype. We also hypothesize that the variant may be linked to additional health conditions, including brachycephalic obstructive airway syndrome and congenital heart defects. Altogether, our study strengthens the role of DVL2 as one of the contributors to the “bulldog type” morphology and features on the spectrum of human Robinow syndrome.

Genetic and Biochemical Predictors of Neonatal Bronchopulmonary Dysplasia

Bronchopulmonary dysplasia (BPD) is a common complication of prematurity with a multifactorial etiology, influenced by both genetic susceptibility and environmental factors on the immature lung. Fibroblast growth factor receptor-3 and -4 (FGFR-3 and FGFR-4) are abundantly expressed in both the epithelium and mesenchyme in the developing mammalian lung. FGFR-4 may play a role in developing BPD as it is associated with airway inflammation and remodeling; studies showed a link between BPD and a polymorphism in the FGFR-4 gene. The aim of this study was to study the significance of FGFR-4 in developing BPD and to investigate the correlation between its serum level and its genetic polymorphism in relation to development of BPD in preterms. This case–control study was performed on 80 preterm neonates (<32 weeks) divided into two groups: group I included 50 preterms with respiratory distress syndrome (RDS) who developed BPD and group II included 30 preterms with RDS only. The mean serum level of FGFR-4 was significantly lower in group I than in group II (p-value < 0.05). There was no significant correlation between the serum levels of FGFR-4 and the degree of severity of BPD. Allele variation in the FGFR-4 gene was similar in both groups. The serum level of FGFR-4 was significantly lower in preterms with BPD, although the gene polymorphism was not significantly different in the studied groups.

Polymorphism scanning of HSP90AB1 gene in local Friesian Holstein as molecular marker for heat stress resistance

Heat stress poses major problem in dairy cattle in term of reproduction and milk yield, especially in humid tropical climates. The HSP90AB1 is a gene that plays important role in heat stress response. Scanning its allele and genotype variation could be beneficial for the selection of dairy cattle which able to cope with heat stress effect. This study aimed to identify HSP90AB1 gene polymorphism (SNP g.4338T>C) in Indonesian local Friesian Holstein dairy cattle population. In total 20 cattle were sampled randomly. In this study, AS-PCR was employed to amplify 561 bp of gene fragment, using pair of primer namely CF primer 5-CTGGAGTCACACTGAGGAAC-3, TF primer 5-CTGGAGTCACA CTGAGGAAT-3, F primer 5-CTGGAGTCACACTGAG-3, and R primer 5-TGTTGGAGATCGTCACCTG-3. As the results, allele T and C were observed, and respective frequencies are 0.35 and 0.65. Three genotypes of HSP90AB1 gene were found namely CC, CT, and TT. The respective genotype frequency is 0.1, 0.5, and 0.4. According to Hardy-Weinberg analysis, the population is in equilibrium (P>0.05). It is concluded that CT genotype and T allele are the highest frequency in the sampled population. Further study needs to be performed to associate the genotype and allele variation to productivity trait of local dairy cattle.

Review on the genetic history of Algerians within North African populations from the HLA point of view

This article aims to take stock of knowledge on the history of the human settlement of North Africa and the genetic history of Algerians within North African populations by gathering the most important published results related to HLA allele analysis. These results revealed a strong genetic relationship between studied North African populations (Algeria, Morocco and Tunisia). Such evident genetic affinity between North African populations, also proved by the use of other powerful autosomal markers, agrees with historic data considering North African populations as having similar origins. HLA allele analysis also indicated a genetic link between North African populations (Algeria, Tunisia and Morocco) and the populations of the South-Western Europe particularly the Basques and Spaniards. This would reflect a Neolithic relationship between Iberians and the natives of North Africa (the Berbers). However, other results showed a genetic distinction between samples from North African populations and Middle Eastern populations (Arab-Palestinians, Lebanese’s and Jordanians). Beside these results related to Mediterranean populations, the HLA allele variation was analyzed at the world scale showing low genetic differentiations among the three broad continental areas, with no special divergence of Africa. Keywords: Genetic diversity; Molecular Anthropology; Genetic History; HLA genes; North Africa; Algeria

Accelerated molecular breeding of novel cytoplasmic male sterility lines in rice using orfH79 or orf290 haplotypes

The identification and development of new cytoplasmic male sterility (CMS) lines in higher plants is important for the preservation of grain security and the prevention of homogenization of hybrid rice. Molecular markers assisted selection (MAS) based on CMS-associated genes or mitochondrial-specific chimeric sequences are important for rapid and effective breeding of new CMS lines and hybrids. In our study, the distribution and allele variation of orfH79 and orf290 genes were characterized from 273 wild and cultivated rice in the AA genome species. Based on the alignment of nucleotide and amino acid sequences, four accessions with orfH79 and three accessions with orf290 were screened. Four novel CMS lines carrying orfH79 haplotypes and three novel CMS lines carrying orf290 haplotypes were then developed using multiple backcross generations with a maintainer line under MAS. The breeding process used in our study provides an efficient and feasible approach for selecting new CMS lines. CMS lines selected in our study are important for enriching rice germplasm resources and guaranteeing rice breeding programs.