Maternal infanticide behavior, a lacking of a clear Mendelian inheritance pattern, could be caused by several genes of low to moderate penetrance, TDT or NPL analysis are hence a more robust and successful alternative to identify susceptible loci for the abnormal behavior. As in other studies [7, 9], we found distinct linkage results between TDT and NPL . NPL test for markers linked to genes affecting disease status on the basis of identity-by-descent, and is more powerful when the marker density is low. TDT is a fine mapping method requiring linkage disequilibrium (LD) between causative mutations and the linked markers [8, 10]. It shows greater power when markers are very close to the causative gene. In this study, the discrepancy between TDT and NPL may be caused by the low marker density and the multiple marker alleles.
Seven candidate genes, of which EAAT2, BDNF, OXTR and 5HTR2C are positional and functional candidate genes, and ESR2, DRD1 and GABRA6 are functional candidate genes, were chosen from five genomic regions including SSC1, SSC2, SSC13, SSC16 and SSCX for further analyzing to find candidate markers linked to sow maternal infanticide behavior. Significant associations were identified on all three ESR2 SNPs, and the overall test of association of the haplotypes also achieved the significance level. Haplotypes of [G;G;T] and [A;A;G] showed very significant transmission disequilibrium between normal and infanticidal sows (P < 0.01). Estrogen and progesterone are important in the initiation of maternal behavior . Estrogens have generally excitatory effects  and considerable regulatory influence on systems mediating anxiety and mood . Sows with high ratio of estrogen to progesterone in late pregnancy showed increased savaging to their piglets . Estrogen's actions could be mediated by estrogen receptor 1 or 2 (α or β). ESR1 is critical for reproduction function, and ESR2 is critically involved in regulating reproductive behaviors, brain development and procession of emotional behavior (anxiety-related behavior e.g.) . This result was also consistent with the results in western commercial sows (personal communication, C. Sargent, University of Cambridge, UK), in which an A/G polymorphism at position 949 nt of ESR2 mRNA was associated with maternal infanticide. However, no QTL was detected on SSC1 in whole genome QTL mapping. It could be caused by low marker density tested on this chromosome.
Another significant association was found on EAAT2 gene. Extreme significance level was achieved both in analyses of g. 233G > A and haplotypes (P < 0.01, Table 2). Although the significant microsatellite marker and EAAT2 gene were not in the same genomic region on SSC2, this result should confirm the existence of QTL on this chromosome owning to large linkage disequilibrium in F2 population. EAAT2 is responsible for the majority of glutamate uptake in the brain and its disregulation has been associated with multiple psychiatric and neurological disorders . Its expression in infanticidal sows from the current population is down-regulated (Data from cDNA microarray analysis, unpublished). Combined with the association result in this study, it is a strong candidate gene for maternal infanticide.
The last significant association was identified on DRD1 gene. DRD1 encodes the D1 subtype of the dopamine receptor. D1 receptors regulate neuronal growth and development, mediates some behavioral responses and schizophrenia [17, 18]. Given the differently transmitted frequency of the DRD1 alleles and its important roles in behavioral responses, DRD1 could be an important candidate gene influencing sow maternal infanticide behavior. The significant association of DRD1 with maternal infanticide indicated that a causative gene may exist within this chromosome region. Only five microsatellite markers on SSC16 were used in the whole genome QTL scanning, therefore the absence of a QTL on this chromosome may be due to low marker density.
Interestingly, the alleles both in SNPs and haplotypes which had overtransmission to infanticidal sows were from White Duroc. This result was also consistent with the previous reports about maternal ability of Chinese and Western pig breeds. The Chinese Erhualian pig breed is the most famous Chinese indigenous pig breed for its excellent reproductive performance. Van der Steen and de Groot (1992) found that Meishan piglets have 5% advantage in survival rate than large white piglets due to good maternal behavior . The Chinese Meishan breed exhibits good maternal characteristics with resulting even heavier piglets at weaning and lower incidence of aggressive behavior towards their offspring than European white sows .
The other candidate genes, such as BDNF, OXTR and GABRA6, which play important roles in the phenotypes similarly to maternal infanticide behavior, for example anxiety-related behavior , mood disorders , depression-related traits  and pressure response , did not show any significant association with maternal infanticide behavior in this study. So these genes are not the candidate genes for maternal infanticide in the White Duroc × Erhualian resource population, or more SNPs in these genes needed to be evaluated. Especially for OXTR gene, in rats, females having a significantly high expression level of oxytocin receptors in several areas of brain showed more maternal care to offspring , and the oxytocin receptor gene located proximal to a QTL on SSC13 detected by both NPL and TDT. However, the QTL on this chromosome only achieved P < 0.05 significance level, false discovery can not be excluded.
For chromosome X, similarly to the results in NPL  and western commercial pig lines , all 15 microsatellite markers showed very significant association with maternal infanticide behavior in the TDT analysis. 5-HTR2C shows close relationship with anxiety-like behavior and major mental disorders including schizophrenia, bipolar disorder and major depression [26, 27]. In this study, allele A of g.675C > T (HM754211) was preferably transmitted to infanticidal sows compared with allele C. The P value did not achieve statistical significant level due to the small population size, or more SNPs in this gene or more candidate genes need to be analyzed.