Classical, Molecular, and Genomic Cytogenetics of the Pig, a Clinical Perspective

Abstract

The chromosomes of the domestic pig (Sus scrofa domesticus) are known to be prone to reciprocal chromosome translocations and other balanced chromosome rearrangements with concomitant fertility impairment of carriers. In response to the remarkable prevalence of chromosome rearrangements in swine herds, clinical cytogenetics laboratories have been established in several countries in order to screen young boars for chromosome rearrangements prior to service. At present, clinical cytogenetics laboratories typically apply classical cytogenetics techniques such as giemsa-trypsin (GTG)-banding to produce high-quality karyotypes and reveal large-scale chromosome ectopic exchanges. Further refinements to clinical cytogenetics practices have led to the implementation of molecular cytogenetics techniques such as fluorescent in-situ hybridization (FISH), allowing for rearrangements to be visualized and breakpoints refined using fluorescently labelled painting probes. The next-generation of clinical cytogenetics include the implementation of DNA microarrays, and next-generation sequencing (NGS) technologies such as DNA sequencing to better explore tentative genome architecture changes. The implementation of these cytogenomics techniques allow the genomes of rearrangement carriers to be deciphered at the highest resolution, allowing rearrangements to be detected; breakpoints to be delineated; and, most importantly, potential gene implications of those chromosome rearrangements to be interrogated. Clinical cytogenetics has become an integral tool in the livestock industry, identifying rearrangements and allowing breeders to make informed breeding decisions.

The Cytogenetics of the Water Buffalo: A Review

“…Conversely, numerical sex chromosome abnormalities are more tolerated by the species, because one of their X chromosomes is genetically inactivated [ 91 ], although some genes seem to escape gene inactivation [ 92 ]. However, numerical sex chromosome abnormalities are often correlated with sterility or low fertility, especially in females [ 3 , 4 , 5 , 6 , 7 ]. Balanced chromosomal abnormalities are generally correlated with reduced fertility due to unbalanced gametes originating during meiosis to form trivalent (centric fusions) or quadrivalent (reciprocal translocations) configurations.…”

“…Balanced chromosomal abnormalities are generally correlated with reduced fertility due to unbalanced gametes originating during meiosis to form trivalent (centric fusions) or quadrivalent (reciprocal translocations) configurations. Subsequently, unbalanced gametes and embryos generally die in early embryonic life [ 3 , 4 , 5 , 6 , 7 ].…”

“…These chromosome changes have been the result of karyotype evolution, determining several species. Furthermore, the study of chromosomes has been mainly used in animal cytogenetics to (1) verify the relationship between chromosome abnormalities and fertility [ 3 , 4 , 5 , 6 , 7 ]; (2) physically map both type I (expressed sequences) and type II (SSRs, microsatellite marker, STSs) loci, especially using fluorescence in situ hybridization (FISH) techniques [ 8 , 9 , 10 , 11 , 12 ]; (3) correctly identify the chromosomes involved in chromosomal abnormalities via chromosome banding techniques [ 13 , 14 ]; (4) reveal chromosome rearrangements occurring in some chromosomal abnormalities, especially using both FISH mapping [ 15 , 16 , 17 ] and comparative genome hybridization array (aCGH) techniques [ 18 , 19 ]; (5) compare related and unrelated genomes by using the Zoo-FISH technique [ 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 ], centromeric SAT sequences by FISH mapping [ 29 ], or detailed FISH mapping along chromosomes [ 30 , 31 , 32 , 33 , 34 , 35 , 36 ]; and (6) test the genome stability of several bovids, including the river buffalo, with both in vitro and in vivo (natural) exposure to potential mutagens [ 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 ], or affected by limb malformation...…”

Balanced Chromosomal Rearrangements Associated with Hypoprolificacy in Australian Boars (Sus scrofa domesticus)

“…The mechanisms of reciprocal translocations are yet to be fully understood. However, recent studies suggest that the likelihood of translocations in the mammalian genome is associated with multiple chromosome features, such as physical length of chromosomes, frequency of translocation breakpoints, presence of common fragile sites, and chromatin density (e.g., heterochromatin or euchromatin) [8,10,[13][14][15][16][17][18][19]. In a recent study, Donaldson et al [20] reported a significant association of translocation frequency to the length of chromosome arms where larger chromosome arms tend to possess more translocation breakpoints.…”

“…In pigs, more than 200 reciprocal translocations have been identified genome-wide, which cause a reduction in litter size up to 50% due to high mortality among early em-bryos [3,8,9]. Published data showed that approximately 50% of boars have hypoprolificacy due to reciprocal translocation with normal semen parameters [9,10]. Reciprocal translocations are heritable and can occur de novo, and do not appear to be line-specific.…”