Previously, we reported a quantitative trait locus (QTL) that affect total teat number (TTN) on pig chromosome 7 (SSC7) in a large F2 intercross population between Landrace and Korean native pigs. The aim of this study was to refine the QTL associated with TTN and to identify positional candidate gene(s) within the refined genomic region. TTN was recorded in 1,105 F2 progeny. All experimental animals were genotyped using 998 informative single nucleotide polymorphism (SNP) markers located on SSC7. A haplotype-based linkage and association analysis using the PHASEBOOK programme was applied to perform high-resolution QTL analysis. Additionally, linear mixed-effect models were used to assess the effect of a positional candidate gene on TTN and other economically important traits [i.e., thoracic vertebrae number (THO), carcass body length (CBL) and weight (CW), back fat thickness (BFT) and intramuscular fat content (IMF) in loin muscles]. Joint linkage and association analysis refined the critical region to a 1.07 Mb region that included a novel positional candidate gene, BRMS1L, that encodes the breast cancer metastasis-suppressor 1-like protein, which could possibly be implicated in normal mammary gland development. Significant association of an SNP marker (g.-1087 G>A) in the 5’-flanking region of BRMS1L with TTN (P=1.10x10-8), THO (P=5.80x10-4), and CBL (P=0.038) was observed. Based on these data, we propose BRMS1L as a positional candidate gene for TTN in pigs. After validation of the association in other independent populations and further functional studies, these results could be useful in optimizing breeding programmes that improve TTN and other economically important traits in swine

In recent years, the efficiency and accuracy of QTL analysis for identification of useful traits have been increased by high-throughput genotyping. In a previous study, the genome variation of significant DNA polymorphism was observed in early maturing type rice mutant (EMT) by comparing with that of wild type (WT). For detection of major QTL for flowering time, we constructed a linkage map of 36 InDel- and 6 SNP- markers. In the linkage analysis of F2 plants derived from the cross “WT x EMT”, we have detected one potential QTL region on chromosome 6 by M6-3 marker. Also, the Hd1, which contained the target fragment of M6-3 marker, exhibited the relatively high nonsynonymous substitutions in genes located on chromosomal region from M6-2 to M6-4. To evaluate the reliable allele segregation related to expected Mendelian ratio between M6-3 and its flanking markers, M6-3 marker developed in Hd1 gene exhibited the 1:2:1 ratio as clear monogenic segregation in heterozygous F3 plant. Additionally, we further analyzed the different transcript regulations of OsGI and Hd3a gene related to Hd1 involved in photoperiodic flowering pathway. Although the mRNA levels of Hd1 had no difference between WT and EMT, the Hd3a as downstream effector of Hd1 significantly upregulated in EMT, suggesting that Hd1 gene may become nonfunctional.

Bakanae disease incidence threat is an increasing trend in the top rice growing countries. Despite it is essential to identify the resistant genes and underlying mechanisms of bakanae disease to develop resistant varieties, there are very limited genetic studies on bakanae disease in rice. The indica rice variety Shingwang was selected as resistant donor to bakanae disease. One hundred sixty nine NILs, YR28297 (BC6F4) generated by five backcrosses of Shingwang with the genetic background of susceptible japonica variety, Ilpum were used for QTL analysis. Rice bakanae disease pathogen, CF283, was mainly used in this study and inoculation and evaluation of bakanae disease was performed with the method of the large-scale screening method developed by Kim et al. (2014). The proportion of healthy plants of Shingwang and Ilpum after inoculation was confirmed using bakanae disease pathogen, CF283. While inoculated Ilpum showed thin and yellowish-green phenotype which is typical symptom of Bakanae disease, Shingwang showed similar healthy phenotype with control plants. A major QTL for resistance against bakanae disease on chromosome 1 was identified using SSR marker, RM9, which explaining 65 % of the total phenotype variation. The major QTL designated as qBK1 and mapped to a 4.4 Mbp region between RM24 (19.30 Mb) and RM11295 (23.72 Mb). The information of qBK1 could be useful for improving rice bakanae disease resistance in marker-assisted breeding.

Using a series of BC8F4 nearly isogenic lines(IL-20) derived from a cross between Hwaseongbyeo, as the recurrent parent, and wild rice Oryza minuta (IRGC Acc. No. 101144) as the donor parent we constructed a high-resolution physical map for the days to heading (dth9)-QTL. dth9 QTL was mapped to the long arm of chromosome 9 across a 34.74-kb region containing 8 predicted genes. Heading date of Japonica rice variety Hwaseongbyeo was one week earlier than a near-isogenic line (NILs) IL-20 under natural field (NF) conditions and 3-4 days under short-day (SD) conditions implying that the dth9-QTL is involved in photoperiod sensitivity in rice. Of the 8 predicted genes three were protein-coding genes in dth9-QTL region. According to RiceXpro published data, micro-array analysis of different leaf developmental stages of Nipponbare showed a higher level of LOC_Os09g36700 mRNA expression during panicle initiation stage. This data further supported our prediction that dth9 locus is responsible for delayed heading in IL-20. Previous studies showed that RNase T2 family proteins are involved in photoperiod sensitivity. Based on these findings we sequenced two candidate genes, which encoded for RNase T2 family proteins. Interestingly, we found the existence of a missense mutation in LOC_Os09g36700 gene suggesting that dth9-QTL might control difference in days to heading between Hwaseongbyeo and IL-20. The QTL for days to heading had not been detected in previous QTL studies between Oryza cultivars, indicating the existence of potentially novel allele from O. mimuta.

In the previous study (Yuan et al. 2009), a quantitative trait locus (QTL) for grain weight was detected on the short arm of chromosome 5 using an advanced backcross lines (BC3F3) between Hwayeongbye (Oryza sativa) and W1944(Oryza rufipogon Griff.) .For detection of gw5 locus, a line CR6 (BC3F4) was selected and crossed to Hwayeongbyeo produce S1F2 and S1F3 population. And a plant from S1F3 population, carried W1944 homozygous segment for target region at gw5 was crossed to Hwayeong to produce S2F2 population. All these population including some S1F3 lines were grown in the field in 2007, 2008 and 2009, respectively (fig1). Frequency distribution of grain weight followed the Mendelian ratios(3:1) for single locus segregation (Χ2=1.22, 0.76, 1.34 in 2007, 2008 and 2009 respectively).In Hwayeongbye genetic background, the W1944 allele at the gw5 locusde creased grain weight, QTL analysis showed that gw5 co-segregated with RM18003 and RM194 (R2=62.7, 69.5 and 37.1% in 2007, 2008 and 2009 respectively). Addition, five QTLs plant height, culm length, secondary branch, spikelet number perplant and rationing ability were detected in the region around gw5, in 2008 and 2009. Substitution mapping with 32F3 lines, gw5 QTL was flanked by two SSRmarkers, RM18003 and RM194, in a300kb to 1.7Mb physical distance region,. QTL analysis indicated that 5 others QTLs plant height, culm length, secondary branch, spikelet number per plant and rationing ability were tightly linked.

Heading date in rice is a complex trait that is governed by multiple genes and environmental factors, such as day-length, temperature, and soil conditions. The genetic studies using DNA markers have facilitated the genetic dissection of heading date and many quantitative trait loci (QTLs) for heading date have been identified using several mapping population. In a previous study, a new quantitative trait loci (QTLs) for heading date have been identified using several mapping population. In a previous study, a new for heading date was detected near SSR marker RM215 on chromosome 9 using an advanced backcross line, WH29001, developed by introgressing chromosomal segments from an accession of Oryzaminuta (2n=48, BBCC, Acc. No.101141)into the O. sativa subsp. japonica cv. Hwaseongbyeo. The O. minuta allele of QTL contributed to an increase in heading date. To clarify whether dth9 could be dissected genetically, a high-resolution linkage mapping of dth9 was performed using alarge F2 population derived form the cross between one F4 plant which was homozygous for O.minuta in the target region RM5661-RM215 on chromosome9 and Hwaseongbyeo. Days to heading in the F2 population showed continuous variation rang form 102 to 113 days. The dth9 QTL further narrowed down at the interval between the SSR marker RM1553 and RM215 which was approximately 403kb in length based on the physical map of the region. The QTL for heading date(dth9) had not been detected in previous QTL studies between Oryza cultivars, indicating the existence of potentially novel alleles from O. minuta.