A review of challenges to genetic improvement of indigenous livestock for improved food production in Nigeria

Indigenous livestock production is intertwined with the life style of Nigerians. The Nigerian livestock industry employs the bulk of the rural work-force, and indigenous livestock breeds are abundant in the industry. These breeds are distributed across the diverse agro-ecological production systems, and are carriers of unique and responsive genotypes shaped by the needs of their managers. Despite their unique features, most indigenous livestock breeds are characteristically low in production and productivity. Improvement of these breeds represents a logical starting point for improving food security and agricultural productivity in Nigeria. To better understand natural genetic variation in these indigenous livestock breeds and strategies for improvement, better genetic characterization is required. Molecular assisted selection (MAS) will be valuable in the pursuit of selection for increased production, but the application of MAS to livestock improvement is constrained by a variety of limitations. The focus of this paper is to elucidate the potential of MAS as a tool for genetic improvement of indigenous livestock, to identify constraints and challenges in MAS implementation and propose solutions to increasing MAS feasibility in pursuit of improved food security and sustainability in Nigeria.Keywords: Food security, Genetic improvement, Genomic Selection, Indigenous livestock, Marker assisted selection, Nigeri

AdaptMap: exploring goat diversity and adaptation

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Casein Gene Cluster in Camelids: Comparative Genome Analysis and New Findings on Haplotype Variability and Physical Mapping

The structure of casein genes has been fully understood in llamas, whereas in other camelids, this information is still incomplete. In fact, structure and polymorphisms have been identified in three (CSN1S1, αs1-CN; CSN2, β-CN; CSN3, κ-CN) out of four casein genes, whereas controversial information is available for the CSN1S2 (αs2-CN) in terms of structure and genetic diversity. Data from the genome analysis, whose assembly is available for feral camel, Bactrian, dromedary, and alpaca, can contribute to a better knowledge. However, a majority of the scaffolds available in GenBank are still unplaced, and the comparative annotation is often inaccurate or lacking.Therefore, the aims of this study are 1) to perform a comparative genome analysis and synthesize the literature data on camelids casein cluster; 2) to analyze the casein variability in two dromedary populations (Sudanese and Nigerian) using polymorphisms at CSN1S1 (c.150G > T), CSN2 (g.2126A > G), and CSN3 (g.1029T > C); and 3) to physically map the casein cluster in alpaca. Exon structures, gene and intergenic distances, large insertion/deletion events, SNPs, and microsatellites were annotated. In all camelids, the CSN1S2 consists of 17 exons, confirming the structure of llama CSN1S2 gene. The comparative analysis of the complete casein cluster (∼190kb) shows 12,818 polymorphisms. The most polymorphic gene is the CSN1S1 (99 SNPs in Bactrian vs. 248 in dromedary vs. 626 in alpaca). The less polymorphic is the CSN3 in the Bactrian (22 SNPs) and alpaca (301 SNPs), whereas it is the CSN1S2 in dromedary (79 SNPs). In the two investigated dromedary populations, the allele frequencies for the three markers are slightly different: the allele C at CSN1S1 is very rare in Nigerian (0.054) and Sudanese dromedaries (0.094), whereas the frequency of the allele G at CSN2 is almost inverted. Haplotype analysis evidenced GAC as the most frequent (0.288) and TGC as the rarest (0.005). The analysis of R-banding metaphases hybridized with specific probes mapped the casein genes on chromosome 2q21 in alpaca. These data deepen the information on the structure of the casein cluster in camelids and add knowledge on the cytogenetic map and haplotype variability

Genetic characterization of the oxytocin-neurophysin I gene (<i>OXT</i>) and its regulatory regions analysis in domestic Old and New World camelids

<div><p>Oxytocin is a neurohypophysial peptide linked to a wide range of biological functions, including milk ejection, temperament and reproduction. Aims of the present study were a) the characterization of the <i>OXT</i> (Oxytocin-neurophysin I) gene and its regulatory regions in Old and New world camelids; b) the investigation of the genetic diversity and the discovery of markers potentially affecting the gene regulation. On average, the gene extends over 814 bp, ranging between 825 bp in dromedary, 811 bp in Bactrian and 810 bp in llama and alpaca. Such difference in size is due to a duplication event of 21 bp in dromedary. The main regulatory elements, including the composite hormone response elements (CHREs), were identified in the promoter, whereas the presence of mature microRNAs binding sequences in the 3’UTR improves the knowledge on the factors putatively involved in the <i>OXT</i> gene regulation, although their specific biological effect needs to be still elucidated. The sequencing of genomic DNA allowed the identification of 17 intraspecific polymorphisms and 69 nucleotide differences among the four species. One of these (MF464535:g.622C>G) is responsible, in alpaca, for the loss of a consensus sequence for the transcription factor SP1. Furthermore, the same SNP falls within a CpG island and it creates a new methylation site, thus opening future possibilities of investigation to verify the influence of the novel allelic variant in the <i>OXT</i> gene regulation. A PCR-RFLP method was setup for the genotyping and the frequency of the allele C was 0.93 in a population of 71 alpacas. The obtained data clarify the structure of <i>OXT</i> gene in domestic camelids and add knowledge to the genetic variability of a genomic region, which has received little investigation so far. These findings open the opportunity for new investigations, including association studies with productive and reproductive traits.</p></div

Polymorphisms detected by the comparison among the complete sequences of <i>OXT</i> gene and the regulatory regions of domestic camelids investigated in the present study (<i>C</i>. <i>dromedarius</i>, <i>C</i>. <i>bactrianus</i>, <i>V</i>. <i>pacos</i>, <i>L</i>. <i>glama</i>).

<p>Polymorphisms detected by the comparison among the complete sequences of <i>OXT</i> gene and the regulatory regions of domestic camelids investigated in the present study (<i>C</i>. <i>dromedarius</i>, <i>C</i>. <i>bactrianus</i>, <i>V</i>. <i>pacos</i>, <i>L</i>. <i>glama</i>).</p

Primer sequences, annealing temperature (T_a) and amplicon size used for the sequencing and genetic diversity discovery at <i>OXT</i> locus in domestic camelids.

<p>Primer sequences, annealing temperature (T_a) and amplicon size used for the sequencing and genetic diversity discovery at <i>OXT</i> locus in domestic camelids.</p

MicroRNA target sequences affected by SNP at 3’UTR.

<p>The transversion C>G (MF464535:g.1682C>G in alpacas and MF464534:g.1731C>G in llamas) falling 19 bp downstream the stop codon (underlined) affects different microRNA target sequences with 8mer (mir-4651, mir-608), 7mer-m8 (mir-6737-5p reported as example, but also mir-6819-5p) and 7mer-A1 (mir-6747-5p, mir-342-5p and mir-4664-5p). Binding of mature miRNAs are shown, whereas the site of the SNP is indicated in bold.</p

Genotyping of the g.622C>G at alpaca <i>OXT</i> promoter.

<p>Genotyping of the SNP MF464535:g.622C>G in the promoter region of <i>Vicugna pacos OXT</i> by <i>Bfo</i> I PCR-RFLP. Line 1, CC homozygous sample; line 3, GG homozygous sample; line 2, heterozygous sample. Line L, Mid Range DNA ladder 100bp-3kb (Jena Bioscience).</p

<i>OXT</i> gene in domestic camelids.

<p>Comparative alignment of the complete nucleotide (nt) sequences of oxytocin-neurophysin I encoding (<i>OXT</i>) gene in domestic camelids. Numbering is relative to the first nucleotide of the first exon (+1) and dashes represent nt identical to those in the first line. In lower cases the 5’- and 3’- Un-Translated Regions (UTR), the polyadenylation signal is dot-underlined. The coding region corresponding to the signal peptide is underlined, whereas the sequence coding for the nonapeptide hormone is indicated in bold, and the neurophysin I is in bold italics. The tripeptide processing signal (GKR) is double underlined and asterisks indicate the stop codon. The duplication event of 21bp in <i>C</i>. <i>dromedarius</i> is wave-underlined. Polymorphic sites within the investigated samples are indicated with R = A/G, S = C/G and Y = C/T.</p

Genetic diversity detected by the sequencing of the <i>OXT</i> gene and its regulatory regions in domestic camelids (<i>C</i>. <i>dromedarius</i>, <i>C</i>. <i>bactrianus</i>, <i>V</i>. <i>pacos</i>, <i>L</i>. <i>glama</i>).

<p>Genetic diversity detected by the sequencing of the <i>OXT</i> gene and its regulatory regions in domestic camelids (<i>C</i>. <i>dromedarius</i>, <i>C</i>. <i>bactrianus</i>, <i>V</i>. <i>pacos</i>, <i>L</i>. <i>glama</i>).</p