The genetics and genomics of the rabbit

The purpose of the book is to present in one location a comprehensive overview of the progress of genetics in the rabbit, with a modern vision that integrates genomics to obtain a complete picture of the state of the art and of the applications in this species, defined according to the multiple uses and multi-faceted places that this species has in applied and fundamental biology. The 18 chapters cover several fields of genetics and genomics: Chapters 1 and 2 present the rabbit within the evolutionary framework, including the systematics, its domestication and an overview of the genetic resources (breeds and lines) that have been developed after domestication. Chapters 3-5 cover the rabbit genome, cytogenetics and genetic maps and immunogenetics in this species. Chapters 6-8 present the genetics and molecular genetics of coat colours, fibre traits and other morphological traits and defects. Chapters 9-13 cover the genetics of complex traits (disease resistance, growth and meat production traits, reproduction traits), reproduction technologies and genetic improvement in the meat rabbits. Chapters 14-18 present the omics vision, the biotech and biomodelling perspectives and applications of the rabbit. This book is addressed to a broad audience, including students, teachers, researchers, veterinarians and rabbit breeders.

A whole genome sequence association study of muscle fiber traits in a White Duroc×Erhualian F2 resource population

Objective: Muscle fiber types, numbers and area are crucial aspects associated with meat production and quality. However, there are few studies of pig muscle fibre traits in terms of the detection power, false discovery rate and confidence interval precision of whole-genome quantitative trait loci (QTL). We had previously performed genome scanning for muscle fibre traits using 183 microsatellites and detected 8 significant QTLs in a White Duroc× Erhualian F2 population. The confidence intervals of these QTLs ranged between 11 and 127 centimorgan (cM), which contained hundreds of genes and hampered the identification of QTLs. A whole-genome sequence imputation of the population was used for fine mapping in this study.Methods: A whole-genome sequences association study was performed in the F2 population. Genotyping was performed for 1,020 individuals (19 F0, 68 F1, and 933 F2). The whole-genome variants were imputed and 21,624,800 single nucleotide polymorphisms (SNPs) were identified and examined for associations to 11 longissimus dorsi muscle fiber traits.Results: A total of 3,201 significant SNPs comprising 7 novel QTLs showing associations with the relative area of fiber type I (I_RA), the fiber number per square centimeter (FN) and the total fiber number (TFN). Moreover, one QTL on pig chromosome 14 was found to affect both FN and TFN. Furthermore, four plausible candidate genes associated with FN (kinase non-catalytic C-lobe domain containing [KNDC1]), TFN (KNDC1), and I_RA (solute carrier family 36 member 4, contactin associated protein like 5, and glutamate metabotropic receptor 8) were identified.Conclusion: An efficient and powerful imputation-based association approach was utilized to identify genes potentially associated with muscle fiber traits. These identified genes and SNPs could be explored to improve meat production and quality via marker-assisted selection in pigs.

Variation in <i>KRTAP6-1</i> affects wool fibre diameter in New Zealand Romney ewes

Variation in KRTAP6-1 has been reported to affect wool fibre traits in Merino cross-breed sheep and Chinese Tan sheep, but little is known about whether these effects persist in other breeds. In this study, variation in KRTAP6-1 was investigated in 290 New Zealand (NZ) Romney ewes sired by 16 different rams. Polymerase chain reaction single-stranded conformational polymorphism (PCR-SSCP) analysis revealed four variants (A, B, E and F) of KRTAP6-1, and nine genotypes (AA, AB, AE, AF, BB, BE, BF, EE and FF) in these ewes. Among the 243 ewes that had genotypes with a frequency of over 5 % (i.e. AA, AB and BB), the presence of A was found to be associated with reduced mean fibre diameter (MFD) and increased coefficient of variation in fibre diameter (CVFD), whereas the presence of B had a trend of association with decreased coarse edge measurement (CEM). A genotype effect was also detected for MFD and CVFD. No associations were detected for fibre diameter standard deviation (FDSD), mean fibre curvature (MFC) and medulation. These results suggest that variation in KRTAP6-1 affects wool fibre diameter in NZ Romney ewes, confirming the finding in Merino cross-breed sheep.

Genetic Variability, Heritability and Correlation Studies in F2 Populations of Upland Cotton

A field experiment was conducted at the experimental area of the Department of Plant Breeding & Genetics, Sindh Agriculture University Tandojam, during the year 2014-2015 in order to carry-out genetic analysis in F2 populations of upland cotton. The trial was laid-out in a Randomized Complete Block Design with four replications. The material was consisted of eight parents and ten F2 populations. The analysis of variance revealed significant differences among the parents and F2 populations for all the traits studied except that fibre length was non-significant in parents. The results further suggested that maximum heritability, higher genetic variances coupled with more genetic gains were expressed by the F2 populations CRIS-134 ´ CRIS-508 and CRIS-134 ´ CIM-598 for 1st sympodial node number; CRIS-134 ´ Neelum- 121 and CRIS-134 ´ CRIS-508 for sympodial branches/plant; CRIS-342 ´ FH-113 for boll weight; CRIS- 342 ´ Neelum-121 for bolls/plant, seed cotton yield/plant, lint % and micronaire value and progenies CRIS-342 ´ MNH-886 followed by CRIS-342 ´ Neelum-121 for staple length. These results also suggested that a number of F2 populations indicated their potential for various seed cotton yield and fibre traits. The phenotypic correlations revealed that most of the traits were significantly and positively associated with seed cotton yield/plant. However, higher correlations of sympodial branches/plant (r = 0.69**) and bolls/ plant (r = 0.82**) with seed cotton yield indicated that both the traits are more reliable as compared to other traits for selection of higher seed cotton yields. Very interestingly, fibre traits like lint%, fibre length and micronaire were also significantly correlated with seed cotton yield, suggesting that fibre quality traits can be improved without compromising on seed cotton yield. Thus, the material under study is very promising and worthy of selection to improve many traits simultaneously.