Polymorphism detection of <i>DGAT1</i> and <i>Lep</i> genes in Anatolian water buffalo (<i>Bubalus bubalis</i>) populations in Turkey

Acyl-CoA: diacylglycerol–acyltransferase 1 (DGAT1) enzyme plays a key role in controlling the synthesis rate triglyceride from diacylglycerol. Leptin (LP, OB, obese) is an important hormone that synthesizes mostly from adipose tissue and regulates glucose metabolism and homeostasis. DGAT1 and Lep genes are closely related to reproduction, growth, milk yield and composition in water buffalo breeds. This study aimed to identify genetic variation in the DGAT1 and Lep gene regions in 150 water buffalo individuals from five different provinces of Turkey using DNA sequencing. A total of 38 nucleotide variations and indels have identified 761 bp long partial intron 2 and exon 3 and 5′ UTR regions of the Lep gene in Anatolian water buffalo populations; 422 bp long partial exon 7–9 and exon 8 regions of DGAT1 gene were amplified and two mutations were defined in the point of 155 and 275 nucleotide that is three genotypes for S allele and Y allele of DGAT1 gene in intron 7 in Anatolian buffalo populations, respectively. These SNPs may have an effect on reproduction, growth, milk yield and composition in water buffalo populations and may prove to be useful for water buffalo breeding.

Four large indels detected by cpTILLING in barley chloroplast mutator seedlings

In a previous work, a polymorphism detection strategy based on mismatch digestion was applied to the chloroplast genome of barley seedlings that carried the chloroplast mutator (cpm) genotype through many generations. Sixty-two different one- or two-nucleotide-polymorphisms were detected along with four large indels: an insertion of 15 bp in the intergenic region between tRNAHis and rps19 genes, a deletion of 620 bp in the psbA gene, a deletion of 79 bp in the intergenic region between rpl33 and rps18 genes and a deletion of 45 bp in the rps3 gene. In the present investigation, we analyzed direct repeats located at the borders of those four large indels. Furthermore, we investigated the consequences of protein expression of large indels located in coding regions. The deletion of 620 bp in the psbA gene was lethal at the second leaf stage when homoplastomic. The deletion of 45 bp in the rps3 gene, which eliminates 15 amino acids, did not affect the viability of the seedlings in homoplastomy. Interestingly, the deleted segment is also lacking in the wild type version of the rps3 gene of maize and sorghum. The presence of direct repeats at the borders of the four large indels suggests that they could have originated by illegitimate recombination. This would be in agreement with a previous hypothesis that the Cpm gene product would correspond to a mismatch repair (MMR) protein devoted to maintain plastome stability by playing fundamental roles in mismatch repair during replication and avoiding illegitimate recombination.

Universal and high-fidelity DNA single nucleotide polymorphism detection based on a CRISPR/Cas12a biochip

A universal and high-fidelity genotyping method based on the clustered regularly interspaced short palindromic repeat (CRISPR) system was performed on the microfluidic point-of-care equipment.

Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin

Background: In Sub-Saharan Africa, Borassus aethiopum Mart. (African fan palm) is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity and population structure of B. aethiopum across nine collection sites spanning the three climatic regions of Benin, West Africa, through the use of microsatellite markers. Results: During a first phase we relied on the reported transferability of primers developed in other palm species. We find that, in disagreement with previously published results, only 22.5% of the markers tested enable amplification of B. aethiopum DNA and polymorphism detection is very low. We thus generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it in a second phase for the de novo detection of microsatellite loci. Among the primer pairs designed to target these, 11 enabled polymorphism detection and were further used for analyzing genetic diversity. Across the nine collection sites, expected heterozygosity (He) ranges from 0.263 to 0.451 with an overall average value of 0.354, showing a low genetic diversity. Analysis of molecular variance (AMOVA) shows that within-site variation accounts for 53% of the genetic variation, and accordingly the low number of migrants and the positive values of the fixation index (F) in sites from both the Central (Sudano-Guinean) and the Southern (Guinean) climatic regions suggest limited gene flow between sites. While we globally observe a weak correlation between genetic and geographic distances, our clustering analyses indicate that B. aethiopum palms from Savè (Center) are genetically more similar to those from the Northern sites than to samples from the other Central sites. Conclusions: In the light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic diversity analyses targeting under-studied species. We also suggest future applications for the molecular resources generated through the present study.