We report the highest density genetic linkage map for a livestock species produced to date. Three published maps for Sus scrofa were merged by genotyping virtually every publicly available microsatellite across a single reference population to yield 1042 linked loci, 536 of which are novel assignments, spanning 2286.2 cM (average interval 2.23 cM) in 19 linkage groups 08 autosomal and X chromosomes, n = 19). Linkage groups were constructed de novo and mapped by locus content to avoid propagation of errors in older genotypes. The physical and genetic maps were integrated with 123 informative loci assigned previously by fluorescence in situ hybridization {FISH). Fourteen linkage groups span the entire length of each chromosome. Coverage of chromosomes 11, 12, 15, and 18 will be evaluated as more markers are physically assigned. Marker-deficient regions were identified only on Ilql.7-qter and 14 cen-ql.2. Recombination rates [cM/Mbp) varied between and within chromosomes. Short chromosomal arms recombined at higher rates than long arms, and recombination was more frequent in telomeric regions than in pericentric regions. The high-resolution comprehensive map has the marker density needed to identify quantitative trait loci [QTL), implement marker-assisted selection or introgression and YAC contig construction or chromosomal microdissection.

Background The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete, and unresolved redundancies, short-range order and orientation errors, and associated misassembled genes limited its utility. Results We present 2 annotated highly contiguous chromosome-level genome assemblies created with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. Conclusions These highly contiguous assemblies plus annotation of a further 11 short-read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.

38The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model with high 39 anatomical and immunological similarity to humans. The draft reference genome (Sscrofa10.2) of a 40 purebred Duroc female pig established using older clone-based sequencing methods was incomplete 41 and unresolved redundancies, short range order and orientation errors and associated misassembled 42 genes limited its utility. We present two annotated highly contiguous chromosome-level genome 43 assemblies created with more recent long read technologies and a whole genome shotgun strategy, 44 one for the same Duroc female (Sscrofa11.1) and one for an outbred, composite breed male 45 (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than 46 Sscrofa10.2. These highly contiguous assemblies plus annotation of a further 11 short read assemblies 47 provide an unprecedented view of the genetic make-up of this important agricultural and biomedical 48 model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference 49 genome for genomic research in pigs. 50 51 Keywords 52Pig genomes, reference assembly, pig, genome annotation 53 54 to the discovery of molecular genetic variants and the development of single nucleotide 59 polymorphism (SNP) chips [1] and enabled efforts to dissect the genetic control of complex traits, 60including responses to infectious diseases [2]. 61 62 Genome sequences are not only an essential resource for enabling research but also for applications 63 in the life sciences. Genomic selection, in which associations between thousands of SNPs and trait 64 variation as established in a phenotyped training population are used to choose amongst selection 65 candidates for which there are SNP data but no phenotypes, has delivered genomics-enabled genetic 66 improvement in farmed animals [3] and plants. From its initial successful application in dairy cattle 67 breeding, genomic selection is now being used in many sectors within animal and plant breeding, 68 including by leading pig breeding companies [4, 5]. 69 70The domestic pig (Sus scrofa) has importance not only as a source of animal protein but also as a 71 biomedical model. The choice of the optimal animal model species for pharmacological or toxicology 72 studies can be informed by knowledge of the genome and gene content of the candidate species 73 including pigs [6]. A high quality, richly annotated genome sequence is also essential when using gene 74 editing technologies to engineer improved animal models for research or as sources of cells and tissue 75 for xenotransplantation and potentially for improved productivity [7, 8]. 76 77The highly continuous pig genome sequences reported here are built upon a quarter of a century of 78 effort by the global pig genetics and genomics research community including the development of 79 recombination and radiation hybrid maps [9, 10], cytogenetic and Bacterial Artificial Chromosome 80 (BAC) physical maps [11, 12] and a draft referenc...

The Chinese Meishan (ME) breed of pig is unique for many reproductive traits. Compared with Western breeds of swine, ME females reach puberty earlier, ovulate more ova per estrus, and have greater uterine capacity, while intact males (boars) have smaller testes and extremely elevated plasma levels of pituitary-derived glycoprotein hormones. In an effort to identify the genetic mechanisms controlling the elevated plasma levels of pituitary-derived glycoprotein hormones [in particular, follicle-stimulating hormone (FSH)] and to determine whether some of these genetic factors are also responsible for differences in other phenotypes, we scanned the entire genome for regions that affected plasma FSH in boars from a Meishan-White Composite (equal contributions of Chester White, Landrace, Large White, and Yorkshire) resource population. Initially, the entire genome of 121 boars was scanned for regions that potentially influenced plasma FSH. The most significant genomic regions were further studied in a total of 436 boars. Three genomic regions located on chromosomes 3, 10, and X apparently possess genes that significantly affect FSH level, and one region provided suggestive evidence for the presence of FSH-controlling genes located on chromosome 8. The region on the X chromosome also affected testes size. Similar genomic regions to those identified on chromosomes 3, 8, and 10 in this study have been identified to affect ovulation rate in female litter mates, supporting the hypothesis that plasma FSH in pubertal boars and ovulation rate in females is controlled by a similar set of genes.

The first integrated physical and genetic linkage map encompassing the entire swine chromosome 7 (SSC7) reveals that the porcine MHC (SLA) spans the centromere. A SLA class !I antigen gene lies on the q arm, whereas class I and !!1 genes lie on the p arm, suggesting that the presence of a centromere within the SLA does not preclude a functional complex. The SLA appears smaller than other mammalian MHC, as the genetic distance across two class !, three class !1, and three class !!i SLA gene markers is only I.I cM. There are significant variations in recombination rates as a function of position along the chromosome, and the SLA lies in the region with the lowest rate. Furthermore, the directed integration approach used in this study was more efficient than previous efforts that emphasized the screening of large insert libraries for random microsatellites.Genetic maps of livestock species are currently being developed to provide a worldwide resource for mapping quantitative trait loci, comparative mapping in evolutionary studies, and mapping of pertinent loci in animal models of human disorders. These objectives require a framework of informative markers that can be genotyped economically. Integration of this framework with a cytogenetic map allows evaluation of coverage, genome size, and recombination rates along the chromosome, as well as establishing syntenic relationships among species. Two linkage maps of swine chromosome 7 (SSC7) have been reported, one that includes 11 Archibald et al. 1995) and one with 17 ) microsatellite markers. The two maps have only one marker in common, and both contain intervals >30 cM. The cytogenetic map includes only four relatively low resolution assignments of linked markers with -30% coverage (Ed-

Ovulation rate is an integral component of litter size in swine, but is difficult to directly select for in commercial swine production. Because a QTL has been detected for ovulation rate at the terminal end of chromosome 8p, genetic markers for this QTL would enable direct selection for ovulation rate in both males and females. Eleven genes from human chromosome 4p16-p15, as well as one physiological candidate gene, were genetically mapped in the pig. Large insert swine genomic libraries were screened, clones were isolated and then screened for microsatellite repeats, and informative microsatellite markers were developed for seven genes (GNRHR, IDUA, MAN2B2, MSX1, PDE6B, PPP2R2C, and RGS12). Three genes (LRPAP1, GPRK2L, and FLJ20425) were mapped using genotyping assays developed from single nucleotide polymorphisms. Two genes were assigned since they were present in clones that contained mapped markers (HGFAC and HMX1). The resulting linkage map of pig chromosome 8 contains markers associated with 14 genes in the first 27 cM. One inversion spanning at least 3 Mb in the human genome was detected; all other differences could be explained by resolution of mapping techniques used. Fourteen of the most informative microsatellite markers in the first 27 cM of the map were genotyped across the entire MARC swine resource population, increasing the number of markers typed from 2 to 14 and more than doubling the number ofgenotyped animals with ovulation rate data (295 to 600). Results from the revised data set for the QTL analysis, assuming breed specific QTL alleles, indicated that the most likely position of the QTL resided at 4.85 cM on the new linkage map (F1,592 = 20.5150, genome-wide probability less than 0.015). The updated estimate of the effect of an allele substitution was -1.65 ova for the Meishan allele. The F-ratio peak was closest to markers for MAN2B2 (4.80 cM) and was flanked on the other side by markers for PPP2R2C. Two positional candidate genes included in this study are MAN2B2 and RGS12. These results validate the presence of a QTL affecting ovulation rate on chromosome 8 and facilitate selection of positional candidate genes to be evaluated.

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SummaryWe report the sequences, sizes, and number of alleles of 414 new porcine microsatellites that were cloned in our laboratory and 21 micro‐satellites derived from GenBank DNA sequences. We also confirm the usefulness of porcine microsatellite primer pairs derived from short interdispersed elements.