Identification of Copy Number Variations in Xiang and Kele Pigs

Xiang and Kele pigs are two well-known local Chinese pig breeds that possess rich genetic resources and have enormous economic and scientific value. We performed a comprehensive genomic analysis of the copy number variations (CNVs) in these breeds. CNVs are one of the most important forms of genomic variation and have profound effects on phenotypic variation. In this study, PorcineSNP60 genotyping data from 98 Xiang pigs and 22 Kele pigs were used to identify CNVs. In total, 172 candidate CNV regions (CNVRs) were identified, ranging from 3.19 kb to 8175.26 kb and covering 80.41 Mb of the pig genome. Approximately 56.40% (97/172) of the CNVRs overlapped with those identified in seven previous studies, and 43.60% (75/172) of the identified CNVRs were novel. Of the identified CNVRs, 82 (47 gain, 33 loss, and two gain-loss events that covered 4.58 Mb of the pig genome) were found only in a Xiang population with a large litter size. In contrast, 13 CNVRs (8 gain and 5 loss events) were unique to a Xiang population with small litter sizes, and 30 CNVRs (14 loss and 16 gain events) were unique to Kele pigs. The CNVRs span approximately 660 annotated Sus scrofa genes that are significantly enriched for specific biological functions, such as sensory perception, cognition, reproduction, ATP biosynthetic processes, and neurological processes. Many CNVR-associated genes, particularly the genes involved in reproductive traits, differed between the Xiang populations with large and small litter sizes, and these genes warrant further investigation due to their importance in determining the reproductive performance of Xiang pigs. Our results provide meaningful information about genomic variation, which may be useful in future assessments of the associations between CNVs and important phenotypes in Xiang and Kele pigs to ultimately help protect these rare breeds.     

SLA-11 mutations are associated with litter size traits in Large White and Chinese DIV pigs

Litter size is an important economic traits in pigs. SLA-11 gene is a member of SLA (swine leukocyte antigen) complex. In our previous study, the SLA-11 gene was differentially expressed in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows. Here, we identified two mutations (c.754-132 T?>?C and c.1421?+?38 T?>?C) in SLA-11 gene and analyzed the associations of two SNPs with litter size traits in Large White (n?=?263) and DIV (n?=?117) sows. The results showed that in Large White pigs, SLA-11 c.754-132?CC sows produced 0.74 and 0.87 more pigs per litter for TNB and NBA of all parities than did TT sows (p?<?.05); In DIV pigs, SLA-11 c.754-132?CC sows produced 1.17 more pigs per litter for TNB of all parities than did TC sows (p?<?.05). In Large White pigs, SLA-11 c.1421?+?38?CC sows produced 0.9 more pigs per litter for TNB of all parities than did TT sows (p?<?.05), while in DIV pigs SLA-11 c.1421?+?38?CC sows produced 0.84 and 0.7 less pigs per litter for TNB and NBA of all parities than did TT sows (p?<?.05). Our research indicated that SLA-11 mutations were potential molecular markers for improving the litter size traits in pigs.     

Mapping of the porcine oestrogen receptor 2 gene and association study with litter size in Iberian pigs

Genes encoding the oestrogen receptors (ESR) are considered candidate genes for prolificacy traits due to the key role these molecules play in the regulation of reproductive physiology. In this paper, we report the assignment of the pig ESR2 gene to porcine chromosome 1 by radiation hybrid mapping. Most of the ESR2 cDNA was sequenced from Iberian pig ovarian RNA samples and one A/G single nucleotide polymorphism (SNP) was found at exon 5, being associated with a Met/Val substitution at position 949. This SNP was genotyped using a PCR-RFLP (Hsp92II) protocol and its potential effect on litter size was evaluated in two Iberian pig populations. However, no statistically significant association between the ESR2 polymorphism and litter size was found.     

Effect of average litter weight in pigs on growth performance,carcass characteristics and meat quality of the offspring as depending on birth weight

Offspring born from normal litter size (10 to 15 piglets) but classified as having lower than average birth weight (average of the sow herd used: 1.46 ± 0.2 kg; mean ± s.d.) carry at birth negative phenotypic traits normally associated with intrauterine growth restriction, such as brain-sparing and impaired myofiber hyperplasia. The objective of the study was to assess long-term effects of intrauterine crowding by comparing postnatal performance, carcass characteristics and pork quality of offspring born from litters with higher (>1.7 kg) or lower (<1.3 kg) than average litter birth weight. From a population of multiparous Swiss Large White sows (parity 2 to 6), 16 litters with high (H = 1.75 kg) or low (L = 1.26 kg) average litter birth weight were selected. At farrowing, two female pigs and two castrated pigs were chosen from each litter: from the H-litters those with the intermediate (H_I = 1.79 kg) and lowest (H_L = 1.40 kg) birth weight, and from L-litters those with the highest (L_H = 1.49 kg) and intermediate (L_I = 1.26 kg) birth weight. Average birth weight of the selected H_I and L_I piglets differed (P < 0.05), whereas birth weight of the H_L- and L_H-piglets were similar (P > 0.05). These pigs were fattened in group pen and slaughtered at 165 days of age. Pre-weaning performance of the litters and growth performance, carcass and meat quality traits of the selected pigs were assessed. Number of stillborn and pig mortality were greater (P < 0.05) in L- than in H-litters. Consequently, fewer (P < 0.05) piglets were weaned and average litter weaning weight decreased by 38% (P < 0.05). The selected pigs of the L-litters displayed catch-up growth during the starter and grower–finisher periods, leading to similar (P > 0.05) slaughter weight at 165 days of age. However, H_L-gilts were more feed efficient and had leaner carcasses than H_I-, L_H- and L_I-pigs (birth weight class × gender interaction P < 0.05). Meat quality traits were mostly similar between groups. The marked between-litter birth weight variation observed in normal size litters had therefore no evident negative impact on growth potential and quality of pigs from the lower birth weight group.     

FSHβ subunit gene is associated with major gene controlling litter size in commercial pig breeds

An insertion fragment in porcine FSHβ subunit gene was cloned by PCR. Sequencing data show that the insertion is a retroposon of 292 bp siting in intronⅠ at the site between +809 and +810 base. Based on these results, a PCR programme was created to genotype animal individuals in different pig breeds at FSHβ locus and polymorphism of FSHβ gene was analyzed. With the combination of genotype and litter size of sows, it was demonstrated that FSHβ locus is closely associated with major gene controlling litter size in commercial pig breeds, such as Yorkshire, Landrace, Durco. Averagely the AA sows give more 1.5 piglets than BB sows do per litter.     

猪雌激素受体（ESR）基因对产仔数性状的影响

猪产仔数是重要的经济性状,产仔数的提高将会大大地增加商品肉猪的产量,给现代养猪生产带来巨大的经济效益。ＥＳＲ基因是影响猪产仔数的主效基因,而且与猪的生长发育性状及酮体性状之间不存在负的基因多效性影响。采用ＰＣＲ－ＲＦＬＰｓ的方法,通过对５个不同品种的、特别是我国地方品种的２６２头母猪进行了基因多态性分析,研究表明ＥＳＲ基因在这种种群对产仔数均有极显著影响,ＥＳＲ位点ＢＢ基因型母猪平均比ＡＡ基因型母     

Identification and differential expression of microRNAs in the ovaries of pigs (Sus scrofa) with high and low litter sizes

Litter size affects profitability in the swine industry. Mammalian ovaries play important roles during reproduction, including ovulation and hormone secretion, which are tightly regulated by specific microRNAs (miRNAs). In this study, we investigated the effects of specific miRNAs on porcine litter size. We compared the ovarian miRNAs of Yorkshire pigs with high (YH) and low (YL) litter sizes using Solexa sequencing technology. We identified 327 and 320 miRNAs in the ovaries of YH and YL pigs respectively. A total of 297 miRNAs were co‐expressed; 30 and 23 miRNAs respectively were specifically expressed in the two libraries. A total of 83 novel miRNAs were predicted; 37 specific miRNAs were obtained, of which 21 miRNAs were upregulated and 16 miRNAs were downregulated in YH compared with YL. Additionally, 19 628 and 19 250 target genes were predicted in the two libraries respectively. The results revealed that specific miRNAs (i.e., miR‐224, miR‐99a, let‐7c, miR‐181c, miR‐214 and miR‐21) may affect porcine litter size. The results of this study will help in gaining understanding of the role of miRNAs in porcine litter size regulation.     

Proteomic analysis of reproduction proteins involved in litter size from porcine placenta

A gel-free and label-free quantitative proteomic approach based on a spectral counting strategy was performed to discover prolificacy-related proteins. Soluble proteins of porcine placenta from small litter size group (SLSG) and large litter size group (LLSG) were extracted and subsequently applied to in-solution tryptic digestion followed by liquid chromatography–tandem mass spectrometry analysis. Six and thirteen proteins were highly expressed in SLSG and LLSG, respectively. Of the dominantly expressed proteins, we chose prolificacy-related proteins such as puromycin-sensitive aminopeptidase (PSA) and retinol-binding protein 4 (RBP4). Western blot analysis confirmed that the processed form (70 kDa) of PSA was more expressed and RBP4 (23 kDa) was dominantly expressed in LLSG. These results indicate that PSA and RBP4 are representative proteins involved in porcine fertility traits, and this finding may help to increase litter size of pigs.     

Association with litter size of new polymorphisms on ESR1 and ESR2 genes in a Chinese-European pig line

The objective of this study was to search for polymorphisms in the coding region of the estrogen receptors 1 and 2 (ESR1 and ESR2 )and to analyze the effects of these variants and the well known intronic ESR1 Pvu II polymorphism on litter size in a Chinese-European pig line. We identified five silent single nucleotide polymorphisms (SNP) in the ESR1 cDNA: c.669T > C (exon 3), c.1227C > T (exon 5), c.1452C > T (exon 7), c.1665T > C and c.1755A > G (exon 8). One pair of these SNP (c.1665T > C and c.1755A > G) co-segregated in the analyzed line, and the SNP c.669T > C showed the same segregation pattern as the Pvu II polymorphism. These polymorphisms were tested in this study, although the c.1452C > T SNP within exon 7 was not analyzed due to its low informativeness. In the ESR2 cDNA, one missense SNP was found within exon 5, which caused an amino acid substitution in the coded protein: "c.949G > A (p.Val317Met)" and was tested on sow litter size. Information on 1622 litter records from 408 genotyped sows was analyzed to determine whether these SNP influenced the total number of piglets born (TNB) or the number of born alive (NBA). The polymorphisms ESR1: [Pvu II; c.669T > C], ESR1: [c.1665T > C; c.1755A > G] and ESR2: c.949G > A showed no statistically significant association with litter size. However, the ESR1: c.1227T allele was significantly associated with TNB. The additive substitution effect was estimated to be 0.40 piglets born per litter (P < 0.03), and no dominance effects were observed. This SNP could be useful in assisted selection for litter size in some pig lines, as a new genetic marker in linkage disequilibrium with the causative mutation.     

Porcine growth differentiation factor 9 gene polymorphisms and their associations with litter size

Growth differentiation factor 9 (GDF9) is expressed in oocytes and is thought to be required for ovarian folliculogenesis.Given this function,GDF9 may be considered as a candidate gene controlling pig ovulate rate.In this study,the complete coding sequence was cloned (encoding a 444 amino acid),intron sequence and partial 5'-UTR of pig GDF9.RT-PCR results showed that GDF9 mRNA is expressed in a wide range of tissues of the ruttish Erhualian pig.The expression levels of GDF9 mRNA in pituitary,ovary,uterus and oviduct are higher in the Erhualian pigs than those in Duroc pigs,especially in pituitary with a significant difference (P＜0.05).Comparative sequencing revealed 12 polymorphisms,including 8 single nucleotide polymorphisms (SNPS) and one 314 bp indel in noncoding regions,and the other 3 SNPS in coding regions.Four polymorphisms,G359C,C1801T,T1806C and 314 bp indel,were developed as markers for further use in population variation and association studies.The G359C polymorphism segregates only in Chinese native pigs,Erhualian and Dahuabai,on the contrary,314 bp indel segregates only in Duroc and Landrace.C1801T and T1806C sites seem to be completely linked and segregate in Erhualian,Dahuabai and Landrace.In a word,GDF9 may be not associated with pig litter size in extensive populations as per the studies of allele distributions of the four polymorphisms and pilot association in four breeds.     

Genome-wide association studies uncover genes associated with litter traits in the pig

Litter traits are critical economic variables in the pig industry as they represent a production indicator that can serve to determine sow fertility. In this study, a genome-wide association study on litter traits, including total number born (TNB), number born alive (NBA), litter birth weight (LBW), average birth weight (ABW), and piglet uniformity (PU), was carried out on two pig breeds (Yorkshire and Landrace). A total of 3 637 pigs of both breeds were genotyped using the GeneSeek GGP Porcine 50K SNP BeadChip. A mixed linear model (MLM) and fixed and random model circulating probability unification (FarmCPU) were employed in the genome-wide association studies for litter traits using combined data from the two pig breeds and data from each breed separately. Additionally, the heritability of traits was estimated using three methods—pedigree-based best linear unbiased prediction (PBLUP), genomic best linear unbiased prediction (GBLUP), and single-step best linear unbiased prediction (ssGBLUP)—and was found to lie between 0.065 and 0.1289, 0.0478 and 0.0938, 0.0793 and 0.0935, 0.1862 and 0.2163, and 0.0327 and 0.0419 for TNB, NBA, LBW, ABW, and PU, respectively. We also compared the genomic prediction accuracies and unbiasedness for litter traits of the three BLUP models. Our results indicated that the ssGBLUP method provided higher predictive accuracies and more rational unbiasedness compared with the PBLUP and GBLUP methodologies. Furthermore, based on their possible roles, eight candidate genes (INHBA, LEPR, HDHD2, CTNND2, RNF216, HMX1, PAPPA2, and NTN1) were identified as being linked with litter traits. In the middle of the test, these genes were found to be connected with pig metabolism and ovulation rate. Our results provide the insights into the genetic architecture of litter traits in pigs, and the potential single nucleotide polymorphisms (SNPs) and candidate genes identified may benefit economic profits in pig-breeding industry and contribute to improve litter traits.     

母猪生殖器官大小和产仔数的分子遗传基础

采用单核苷酸多态分析技术（SNP）分析母猪3个生殖激素受体基因（ESR、PRLR和FSHR）的变异,屠宰103头母猪并测定其生殖器官大小;统计母猪的产仔数;利用SAS或SPSS分析软件分析基因变异与母猪的生殖器官大小,产仔数多少的连锁关系,以探讨母猪生殖器官大小和产仔数多少的分子遗传基础,结果表明,如母猪携带的基因型为位点,ESR的BB型,位点FSHRB的BB型,位点ESRB的AA型,位点PRLR的AA型,则母猪的生殖器官较大,产仔数也较多;在位点ESRB或位点PRLR中,带有AA基因型母猪不仅产仔数显著地高于AB、BB型,而且生殖器官也显著大于AB、BB型;在位点ESR和FSHRB中,带有BB基因型母猪的生殖器官,产仔数显著高于带有AB或AA型母猪。     

Genome-wide association analysis reveals genomic regions on Chromosome 13 affecting litter size and candidate genes for uterine horn length in Erhualian pigs

Litter size has a great impact on the profit of swine producers. Uterine development is an important determinant of reproduction efficiency and could hence affect litter size. Chinese Erhualian pig is one of the most prolific breeds in the world, even though large phenotypic variation in litter size was observed within Erhualian sows. To dissect the genetic basis of the phenotypic variation, we herein conducted genome-wide association studies for total number born and number born alive (NBA) of Erhualian sows. In total, one significant single nucleotide polymorphism (SNP) (P<1.78e−06) and 11 suggestive SNPs (P<3.57e−05) were identified on 10 chromosomes, confirming seven previously reported quantitative trait loci (QTL) and uncovering six QTL for litter size or uterus length. One locus on Sus scrofa chromosome (SSC) 13 (79.28 to 90.43 Mb) harbored a cluster of suggestive SNPs associated with multiparous NBA. The SNP (rs81447100) within this region was confirmed to be significantly (P<0.05) associated with litter size in Erhualian (n=313), Sutai (n=173) and Yorkshire (n=488) populations. Retinol binding protein 2 and retinol binding protein 1 functionally related to the development of uterus were located in a region of 2 Mb around rs81447100. Moreover, four genes related to embryo implantation and development were also detected around other significant SNPs. Taken together, our findings provide a potential marker (rs81447100) for the genetic improvement of litter size not only in Chinese Erhualian pigs but also in European commercial pig breeds like Yorkshire, and would facilitate the final identification of causative variant(s) underlying the effect of SSC13 QTL on litter size.     

Effect of Single Nucleotide Polymorphisms in IGFBP2 and IGFBP3 Genes on Litter Size Traits in Berkshire Pigs

Litter size is among the most important traits in swine breeding. However, information on the genetics of litter size in pigs is lacking. In this study, we identified single nucleotide polymorphisms (SNPs) in the insulin-like growth factor binding protein 2 and 3 (IGFBP2 and IGFBP3) genes in Berkshire pigs and analyzed their association with litter size traits. The IGFBP2 SNP was located on chromosome 15 intron 2 (455, A?>?T) and the IGFBP3 SNP was on chromosome 18 intron 2 (53, A?>?G). The AT type of IGFBP2 and the GG type of IGFBP3 had the highest values for all litter size traits including total number born (TNB), number of pigs born alive, and breeding value according to TNB. Homozygous GG pigs expressed higher levels of IGFBP3 mRNA in the endometrium than pigs of other genotypes, and a positive correlation was observed between litter size traits and IGFBP3 but not IGFBP2 expression level. These results suggest that SNPs in the IGFBP2 and the IGFBP3 gene are useful biomarkers for increasing the reproductive productivity of Berkshire pigs.     

猪雌激素受体基因Pvu II多态性与产仔数性状的关系

雌激素受体（estrogen receptor,ESR）能调控雌激素的合成,影响繁殖功能。将ESR基因作为控制猪产仔数的候选基因,分析其Pvu II多态性与高产猪种莱芜猪和国外引进猪种长白猪产仔数的关系。序列分析发现,PCR扩增区56bp的Pvu II酶切片段位于RFLP分析获得的37kb正向序列的起始部分。因ESR基因在高产仔数的莱芜猪中的Pvu II多态性分布不能证实B基因为优势基因,故推测37kb条带对该猪种产仔数可能不起决定作用。 Abstract:Estrogen receptor (ESR) can regulate the synthesis of oestrogen and affect the reproduction of swine.The relationship between PvuII polymorphisms at estrogen receptor gene and litter size was analyzed in Laiwu breed and Landrace breed by candidate gene method.The results were shown that 56bp of PvuII polymorphisms was the same as the beginning sequence of 37kb of RFLP.The distribution of PvuII polymorphisms also could not prove that B gene was a superior gene,and there was no decisive effect of 37kb band on litter size in pigs.     

Genetic determinism for within-litter birth weight variation and its relationship with litter weight and litter size in the Ripollesa ewe breed

Birth weight plays a central role in lamb survival and growth, and the knowledge of its genetic determinism has become essential in worldwide selection programmes. Within this context, within-litter birth weight variation (BWV) has been suggested as an attractive trait to homogenise litters in prolific species, although it has not been analysed in sheep. The objective of this study was to ascertain whether maternal additive genetic variance exists for BWV in Ripollesa ewes, and to study its genetic, permanent environmental and residual relationships with litter weight (LW) and litter size (LS) at birth. Data were recorded in the Ripollesa experimental flock of the Universitat Autònoma of Barcelona, between 1986 and 2005, and included 1 662 litters from 380 ewes, with 712 records of BWV and 1 530 records of LW. Traits were analysed with a multivariate animal model solved through Bayesian methodologies, and with a threshold characterisation of LS. Additionally, the effect of BWV on lamb survival was studied. Additive genetic variance was observed for BWV (h² = 0.061), as well as for LW (h² = 0.200) and LS (h² = 0.141). Nevertheless, genetic correlations among those traits were not substantial (BWV and LW = 0.151; BWV and LS = − 0.219; LW and LS = − 0.320) and suffered from a high degree of uncertainly, with the null correlation included within the highest posterior interval at 95%. Within-litter birth weight variation and LS showed a negative and large permanent environmental correlation ( − 0.872), and LW and LS were negatively correlated due to residual ( − 0.762) and permanent environmental ( − 0.449) random sources of variation. Within-litter birth weight variation influenced lamb mortality during the first 7 days of life (P < 0.05), increasing and decreasing survivability in heavier and lighter littermates, respectively. Nevertheless, stillbirths and lambs died after the 1st week of life were not affected by BWV (P>0.05). The low heritability found indicates that slow genetic progress may be expected from selecting for BWV. Close to zero genetic correlations suggest that this selection will probably not affect LS and LW, although some significant permanent and residual correlations must be taken into account. Further studies are needed to understand better the genetic architecture among these three reproductive traits.     

高山森林林窗对凋落叶分解的影响

林窗对降水和光照等环境条件的再分配以及分解者群落的影响可能深刻作用于森林凋落物分解过程,但有关高山森林林窗大小对凋落物分解的影响尚无研究报道。采用凋落物分解袋法,研究了川西高山森林不同大小林窗对非生长季节和生长季节红桦(Betula albo-sinensis)和岷江冷杉(Abies faxoniana)凋落叶质量损失的影响。结果显示,经过1a的分解,不同生境下红桦和岷江冷杉凋落叶分别分解了27.25%—30.12%和27.04%—27.96%,其中非生长季节占53.83%—60.18%和50.23%—59.09%。林窗对红桦和岷江冷杉凋落叶质量损失的影响因物种不同而呈现季节差异。总体上,林窗加快了岷江冷杉凋落叶的分解而延缓了红桦凋落叶的分解。与郁闭林下相比,林窗显著增加了2种凋落叶非生长季节的质量损失速率,显著降低了生长季节2种凋落叶的质量损失速率;2种凋落叶质量损失速率在非生长季节随林窗面积增大而加快,在生长季节随林窗面积增大而减慢。林窗显著影响了初冻期、深冻期和融化期岷江冷杉凋落叶的质量损失率,但对红桦凋落叶质量损失率影响不显著。可见,高山森林凋落物分解过程受到林窗的显著影响,并且阔叶和针叶凋落叶在非生长季节和生长季节对林窗的响应具有明显差异。     

不同起源时间的植物叶凋落物在中亚热带的分解特性

选择9种起源时间不同的植物的凋落叶,采用分解袋法,在浙江千岛湖地区从2006年6月到2008年6月进行了分解试验,试图探索植物进化过程中凋落物分解特性的演变趋势.所选的9种植物分属于4个类群,按起源时间由早到晚依次为蕨类植物(芒萁和桫椤)、裸子植物(苏铁、水杉、杉木和马尾松)、双子叶植物(木荷和青冈)及单子叶植物(毛竹).每隔一个月取样,每种凋落物3次重复.结果表明:不同植物类群凋落物基质的氮(N)、木质素(Lignin)含量及Lignin/N比值与分解速率具有良好的相关性.起源时间越晚的植物凋落物的基质N含量越高,为单子叶植物>双子叶植物>裸子植物>蕨类植物.Lignin含量和Lignin/N比值的趋势一致,均为起源时间越晚而值越低,即蕨类植物>裸子植物>双子叶植物>单子叶植物.凋落物分解系数k值的范围在0.25～0.63之间,表现出毛竹>青冈>木荷>水杉>马尾松>杉木>苏铁>桫椤>芒萁的趋势.4个植物类群的凋落物分解速率的均值为单子叶植物>双子叶植物>裸子植物>蕨类植物.试验结果初步表明:植物凋落物分解的进化趋势是由分解缓慢逐渐演变为分解较快.     

Genomic prediction of reproduction traits for Merino sheep

Economically important reproduction traits in sheep, such as number of lambs weaned and litter size, are expressed only in females and later in life after most selection decisions are made, which makes them ideal candidates for genomic selection. Accurate genomic predictions would lead to greater genetic gain for these traits by enabling accurate selection of young rams with high genetic merit. The aim of this study was to design and evaluate the accuracy of a genomic prediction method for female reproduction in sheep using daughter trait deviations (DTD) for sires and ewe phenotypes (when individual ewes were genotyped) for three reproduction traits: number of lambs born (NLB), litter size (LSIZE) and number of lambs weaned. Genomic best linear unbiased prediction (GBLUP), BayesR and pedigree BLUP analyses of the three reproduction traits measured on 5340 sheep (4503 ewes and 837 sires) with real and imputed genotypes for 510 174 SNPs were performed. The prediction of breeding values using both sire and ewe trait records was validated in Merino sheep. Prediction accuracy was evaluated by across sire family and random cross‐validations. Accuracies of genomic estimated breeding values (GEBVs) were assessed as the mean Pearson correlation adjusted by the accuracy of the input phenotypes. The addition of sire DTD into the prediction analysis resulted in higher accuracies compared with using only ewe records in genomic predictions or pedigree BLUP. Using GBLUP, the average accuracy based on the combined records (ewes and sire DTD) was 0.43 across traits, but the accuracies varied by trait and type of cross‐validations. The accuracies of GEBVs from random cross‐validations (range 0.17–0.61) were higher than were those from sire family cross‐validations (range 0.00–0.51). The GEBV accuracies of 0.41–0.54 for NLB and LSIZE based on the combined records were amongst the highest in the study. Although BayesR was not significantly different from GBLUP in prediction accuracy, it identified several candidate genes which are known to be associated with NLB and LSIZE. The approach provides a way to make use of all data available in genomic prediction for traits that have limited recording.