Jothi Malar Panandam

Mapping quantitative trait loci (QTLs) for fatty acid composition in an interspecific cross of oil palm.

BackgroundMarker Assisted Selection (MAS) is well suited to a perennial crop like oil palm, in which the economic products are not produced until several years after planting. The use of DNA markers for selection in such crops can greatly reduce the number of breeding cycles needed. With the use of DNA markers, informed decisions can be made at the nursery stage, regarding which individuals should be retained as breeding stock, which are satisfactory for agricultural production, and which should be culled. The trait associated with oil quality, measured in terms of its fatty acid composition, is an important agronomic trait that can eventually be tracked using molecular markers. This will speed up the production of new and improved oil palm planting materials.ResultsA map was constructed using AFLP, RFLP and SSR markers for an interspecific cross involving a Colombian Elaeis oleifera (UP1026) and a Nigerian E. guinneensis (T128). A framework map was generated for the male parent, T128, using Joinmap ver. 4.0. In the paternal (E. guineensis) map, 252 markers (199 AFLP, 38 RFLP and 15 SSR) could be ordered in 21 linkage groups (1815 cM). Interval mapping and multiple-QTL model (MQM) mapping (also known as composite interval mapping, CIM) were used to detect quantitative trait loci (QTLs) controlling oil quality (measured in terms of iodine value and fatty acid composition). At a 5% genome-wide significance threshold level, QTLs associated with iodine value (IV), myristic acid (C14:0), palmitic acid (C16:0), palmitoleic acid (C16:1), stearic acid (C18:0), oleic acid (C18:1) and linoleic acid (C18:2) content were detected. One genomic region on Group 1 appears to be influencing IV, C14:0, C16:0, C18:0 and C18:1 content. Significant QTL for C14:0, C16:1, C18:0 and C18:1 content was detected around the same locus on Group 15, thus revealing another major locus influencing fatty acid composition in oil palm. Additional QTL for C18:0 was detected on Group 3. A minor QTL for C18:2 was detected on Group 2.ConclusionThis study describes the first successful detection of QTLs for fatty acid composition in oil palm. These QTLs constitute useful tools for application in breeding programmes.

Genetic parameters for growth performance of the Malaysian local goats and their crossbreds with the German (improved) Fawn goats

SUMMARY Growth performance data of the local goats of Malaysia and their crossbreds with the German (Improved) Fawn goats were analysed using animal models with maternal effects, in order to estimate additive genetic and crossbreeding parameters. Two different genetic models, the Dickerson (1969, 1973) model and the Kinghorn (1980, 1983) model, were used to estimate crossbreeding parameters. Coefficients of additive breed, heterosis (dominance), and recombination (epistatic) loss were fitted in the animal models as covariates. In general, the individual breed effects for birth, 6-month, and 9-month weights, and maternal breed effects for traits until weaning, were significant, indicating large differences for growth performance between the German Fawn and the local breeds. Heterosis effects by the Dickerson model were small and non-significant, while dominance effects by the Kinghorn model, for some of traits, were large and significant. Highly significant individual recombination loss effects by the Dickerson model, and epistatic loss effects by the Kinghorn model, were obtained for birth and 9-month weights. The estimates of total heritability by an animal model incorporating maternal effects were moderate (0.18-0.35). The differences between heritabilities, estimated by different genetic models (the Dickerson model vs. the Kinghorn model), were small. ZUSAMMENFASSUNG: Genetische Parameter von Wachstumseigenschaften Malaysischer Lokalziegen und ihrer Kreuzung mit Deutscher Rehbrauner Ziege Die Daten wurden mittels Tiermodellen mit Maternalwirkung zur Schätzung additiv genetischer und Kreuzungsparameter analysiert. Zur Schätzung letzterer wurden Modelle von Dickerson (1969, 1973) und Kinghorn (1980, 1983) angewendet. Koeffizienten der additiven Rassenwirkungen, Heterosis (Dominanz) und Rekombinations-wirkungen wurden im Tiermodell als Kovarialbe berücksichtigt. Im allgemeinen waren individuelle Rassenwirkungen für Geburts-, 6- und 9-Monatsgewicht und maternale Rassenwirkungen für Merkmale während der Säugezeit signifikant, eine Folge großer Rassenunterschiede. Das Dickerson Modell führte zu geringen, nicht signifikanten Heterosiswirkungen, während beim Kinghorn Modell diese sich für mehrere Merkmale als groß und signifikant erwiesen haben. Hoch signifikante individuelle Rekombinationsverluste und epistatische Verluste ergaben sich bei beiden Modellen für Geburtsgewicht und 9 Monatsgewicht. Heritabilitätswerte waren mäßig hoch (0.18 bis 0.35), enthielten auch die maternalen Wirkungen und unterschieden sich zwischen beiden Modellen nur geringfügig.

Evidence for a higher number of species of Odontotermes (Isoptera) than currently known from Peninsular Malaysia from mitochondrial DNA phylogenies.

Termites of the genus Odontotermes are important decomposers in the Old World tropics and are sometimes important pests of crops, timber and trees. The species within the genus often have overlapping size ranges and are difficult to differentiate based on morphology. As a result, the taxonomy of Odontotermes in Peninsular Malaysia has not been adequately worked out. In this study, we examined the phylogeny of 40 samples of Odontotermes from Peninsular Malaysia using two mitochondrial DNA regions, that is, the 16S ribosomal RNA and cytochrome oxidase subunit I genes, to aid in elucidating the number of species in the peninsula. Phylogenies were reconstructed from the individual gene and combined gene data sets using parsimony and likelihood criteria. The phylogenies supported the presence of up to eleven species in Peninsular Malaysia, which were identified as O. escherichi, O. hainanensis, O. javanicus, O. longignathus, O. malaccensis, O. oblongatus, O. paraoblongatus, O. sarawakensis, and three possibly new species. Additionally, some of our taxa are thought to comprise a complex of two or more species. The number of species found in this study using DNA methods was more than the initial nine species thought to occur in Peninsular Malaysia. The support values for the clades and morphology of the soldiers provided further evidence for the existence of eleven or more species. Higher resolution genetic markers such as microsatellites would be required to confirm the presence of cryptic species in some taxa.

The effects of polymorphisms in IL-2, IFN-γ, TGF-β2, IgL, TLR-4, MD-2, and iNOS genes on resistance to Salmonella Enteritidis in indigenous chickens

Salmonella Enteritidis is a major cause of food poisoning worldwide, and poultry products are the main source of S. Enteritidis contamination for humans. Among the numerous strategies for disease control, improving genetic resistance to S. Enteritidis has been the most effective approach. We investigated the association between S. Enteritidis burden in the caecum, spleen, and liver of young indigenous chickens and seven candidate genes, selected on the basis of their critical roles in immunological functions. The genes included those encoding interleukin 2 (IL-2), interferon-γ (IFN-γ), transforming growth factor β2 (TGF-β2), immunoglobulin light chain (IgL), toll-like receptor 4 (TLR-4), myeloid differentiation protein 2 (MD-2), and inducible nitric oxide synthase (iNOS). Two Malaysian indigenous chicken breeds were used as sustainable genetic sources of alleles that are resistant to salmonellosis. The polymerase chain reaction restriction fragment-length polymorphism technique was used to genotype the candidate genes. Three different genotypes were observed in all of the candidate genes, except for MD-2. All of the candidate genes showed the Hardy–Weinberg equilibrium for the two populations. The IL-2-MnlI polymorphism was associated with S. Enteritidis burden in the caecum and spleen. The TGF-β2-RsaI, TLR-4-Sau 96I, and iNOS-AluI polymorphisms were associated with the caecum S. Enteritidis load. The other candidate genes were not associated with S. Enteritidis load in any organ. The results indicate that the IL-2, TGF-β2, TLR-4, and iNOS genes are potential candidates for use in selection programmes for increasing genetic resistance against S. Enteritidis in Malaysian indigenous chickens.

Novel SNPs in heat shock protein 70 gene and their association with sperm quality traits of Boer goats and Boer crosses

The semen quality of bucks affects the reproduction performance of the herd and is influenced by genetic and non-genetic factors. Heat shock protein 70 (HSP70) is considered as an important gene affecting semen quality traits. The objectives of this study are to find single nucleotide polymorphisms in HSP70 coding region and their association with semen quality traits on Boer and Boer cross bucks. DNA isolated from 53 goats (36 pure South African Boer and 17 Boer crosses) was subjected to PCR amplification of the exon 1 region of the caprine HSP70 gene. Single-strand conformation polymorphism (SSCP) was used to detect polymorphisms and the variant DNA fragments were sequenced. Two synonymous SNPs (74A>C (ss836187517) and 191C>G (ss836187518)) were detected. Qualities of fresh and post-thaw semen were evaluated for sperm concentration, semen volume, sperm motility and velocity traits, live sperm percentage, and abnormal sperm rate. The C allele of ss836187517 and G allele of ss836187518 were at higher frequencies in both the breeds. The C allele of ss836187517 appeared to be the favorable allele for semen concentration, progressive motility of fresh semen, and motility and sperm lateral head displacement of post-thaw semen. A negative overdominance was observed for ss836187517 alleles on velocity traits of post-thaw semen. The C allele of ss836187518 was favorable for sperm concentration and progressive motility. Results herein suggest that the SNPs in HSP70 may affect on semen quality in tropical regions and specially on the potential of semen for freezing.

Effect of parental genotypes and paternal heterosis on litter traits in crossbred goats

The effect of parental genotype and paternal heterosis on litter size (LS), total litter birth weight (TLW) and average litter birth weight (ALW) was analysed utilizing data from a crossbreeding programme involving the exotic German Fawn goats and local Katjang goats in Malaysia. In this study, these traits were regarded as traits of the litter to consider the effect of service sire genotype. The results revealed that LS was significantly influenced by the genotype of sire. The genotypes of sire and dam had significant effects on TLW and ALW. Estimates of crossbreeding parameter showed significant and negative influence of paternal heterosis on TLW and ALW while there was no significant effect of paternal heterosis on LS. The results of this study stress the need to reconsider the use of local males in the tropics.

Identification of quantitative trait locus (QTL) linked to dorsal fin length from preliminary linkage map of molly fish, Poecilia sp.

A preliminary linkage map was constructed by applying backcross and testcross strategy using microsatellite (SSR) markers developed for Xiphophorus and Poecilia reticulata in ornamental fish, molly Poecilia sp. The linkage map having 18 SSR loci consisted of four linkage groups that spanned a map size of 516.1cM. Association between genotypes and phenotypes was tested in a random fashion and QTL for dorsal fin length was found to be linked to locus Msb069 on linkage group 2. Coincidentally, locus Msb069 was also reported as putative homologue primer pairs containing SSRs repeat motif which encoded hSMP-1, a sex determining locus. Dorsal fin length particularly in males of Poecilia latipinna is an important feature during courtship display. Therefore, we speculate that both dorsal fin length and putative hSMP-1 gene formed a close proximity to male sexual characteristics.

Influence of pre-slaughter transportation and stocking density on carcass and meat quality characteristics of Boer goats

Abstract There are limited studies on the effects of transportation stress and stocking density under tropical conditions and their interactions with aging and muscle types on carcass and meat quality characteristics of goat. The present study investigated the effects of transportation and stocking density on carcass characteristics and meat quality traits of Longissimus dorsi, and Semimembranosus muscles in Boer goats. Thirty 1-year-old Boer goats, divided into two groups, were transported by road for 3.5 h, with density of 0.4 m2 and 0.2 m2 per animal, respectively; a third group which was not transported served as control. Meat pH, drip loss, cooking loss, tenderness and colour were measured from samples of the muscles. The transported goats had significantly lower carcass shrinkage, glycogen content, drip loss, tenderness, lightness, yellowness, hue-angle and chroma values compared to the non-transported group. In contrast, they showed significantly higher cooking loss and redness than the non-transported goats. Goats transported in high stocking density showed significantly (p < .05) higher live weight loss and lower dressing-out percentage than those in low stocking density. This study indicated that higher stocking density at pre-slaughter transportation increased shrinkage loss and deteriorated meat quality of goats. Therefore, using an appropriate density during transportation should be considered.

Demarcation of informative chromosomes in tropical sweet corn inbred lines using microsatellite DNA markers

A study of genetic variation among 10 pairs of chromosomes extracted from 13 tropical sweet corn inbred lines, using 99 microsatellite markers, revealed a wide range of genetic diversity. Allelic richness and the number of effective alleles per chromosome ranged from 2.78 to 4.33 and 1.96 to 3.47, respectively, with respective mean values of 3.62 and 2.73. According to the Shannon’s information index (I) and Nei’s gene diversity coefficient (Nei), Chromosome 10 was the most informative chromosome (I = 1.311 and Nei = 0.703), while Chromosome 2 possessed the least (I = 0.762 and Nei = 0.456). Based on linkage disequilibrium (LD) measurements for loci less than 50 cM apart on the same chromosome, all loci on Chromosomes 1, 6 and 7 were in equilibrium. Even so, there was a high proportion of genetic variation in Chromosomes 4, 5, 8, 9 and 10, thereby revealing their appropriateness for use in the genetic diversity investigations among tropical sweet corn lines. Chromosome 4, with the highest number of loci in linkage disequilibrium, was considered the best for marker-phenotype association and QTL mapping, followed by Chromosomes 5, 8, 9 and 10.

Association of novel SNPs in gonadotropin genes with sperm quality traits of Boer goats and Boer crosses

ABSTRACT The present study aimed to investigate single-nucleotide polymorphisms (SNPs) of caprine FSHβ and caprine LHβ genes and to determine effects of the SNPs on fresh and post-thaw semen quality traits of Boer and Boer-crossbred bucks. The single-strand conformation polymorphism analysis and comparative sequencing revealed three SNPs in exon 3 of caprine follicle-stimulating hormone beta (FSHβ), including, three SNPs; 200A > G (FSHβ3-a), 226T > C (FSHβ3-b), and 237A > G (FSHβ3-c), while two of them (FSHβ3-a and FSHβ3-b) were novel. Furthermore, one SNP in exon 2 of luteinizing hormone beta (LHβ) (207T > C) (LHβ2) was detected. The associations of the four detected SNPs with quality traits of fresh and post-thaw semen were evaluated. Analyses of variance revealed significant association of the candidate genes with libido and semen quality traits. The three SNPs of FSHβ3 had significant effect on libido, progressive motility, and abnormality of fresh semen (P < .05), and on the motility, velocity, and viability traits of post-thaw semen (P < .05). LHβ2 polymorphism only showed association with sperm viability of post-thaw semen. The results of the present study suggest that the SNPs in caprine FSHβ and LHβ are associated with semen quality of male goats.