• Asian-Australasian Journal of Animal Sciences
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• v.29 no.11
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• pp.1555-1561
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• 2016

Shank skin color of Korean native chicken (KNC) shows large color variations. It varies from white, yellow, green, bluish or grey to black, whilst in the majority of European breeds the shanks are typically yellow-colored. Three shank skin color-related traits (i.e., lightness [$L^*$], redness [$a^*$], and yellowness [$b^*$]) were measured by a spectrophotometer in 585 progeny from 68 nuclear families in the KNC resource population. We performed genome scan linkage analysis to identify loci that affect quantitatively measured shank skin color traits in KNC. All these birds were genotyped with 167 DNA markers located throughout the 26 autosomes. The SOLAR program was used to conduct multipoint variance-component quantitative trait locus (QTL) analyses. We detected a major QTL that affects $b^*$ value (logarithm of odds [LOD] = 47.5, $p=1.60{\times}10^{-49}$) on GGA24 (GGA for Gallus gallus). At the same location, we also detected a QTL that influences $a^*$ value (LOD = 14.2, $p=6.14{\times}10^{-16}$). Additionally, beta-carotene dioxygenase 2 (BCDO2), the obvious positional candidate gene under the linkage peaks on GGA24, was investigated by the two association tests: i.e., measured genotype association (MGA) and quantitative transmission disequilibrium test (QTDT). Significant associations were detected between BCDO2 g.9367 A>C and $a^*$ ($P_{MGA}=1.69{\times}10^{-28}$; $P_{QTDT}=2.40{\times}10^{-25}$). The strongest associations were between BCDO2 g.9367 A>C and $b^*$ ($P_{MGA}=3.56{\times}10^{-66}$; $P_{QTDT}=1.68{\times}10^{-65}$). However, linkage analyses conditional on the single nucleotide polymorphism indicated that other functional variants should exist. Taken together, we demonstrate for the first time the linkage and association between the BCDO2 locus on GGA24 and quantitatively measured shank skin color traits in KNC.

• Korean Journal of Animal Reproduction
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• v.25 no.4
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• pp.295-304
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• 2001

Characterization of quantitative trait loci (QTL) was investigated in the experimental crosses between Berkshire and Yorkshire breed. A total of 525 F$_2$ progenies from 65 matting of F$_1$ Parents were produced. Phenotypic measurements included average daily gain (ADG), average back fat thickness (ABF), and loin eye area (LEA). To identify the presence of QTL for reproductive performance, birth weight (BWT) and body weight at 16 days (16DAY) were included as indirect trait. QTL segregation was deduced using 8 markers assigned to chromosome 2 (SSC2). Quantitative trait locus analyses were performed using interval mapping by regression under line-cross model. Presence of imprinting was tested under the statistical model that separated the expression of paternally and maternally inherited alleles. To set the evidence of QTL presence, significance thresholds were derived by permutation following statistical tests, respectively. Genome scan revealed significant evidence for three quantitative trait loci (QTL) affecting growth and body compositions, of which two were identified to be QTL with imprinting expression mode near the ICF II gene region. For average back fat thickness (ABF), a paternally expressed QTL was found on chromosome 2 (SSC2). A paternally expressed QTL affecting loin eye area (LEA) was found in the region of SSC2 where evidence of imprinted QTL was found for average back fat thickness (ABF). For average daily gain (ADG), QTL expressed with Mendelian mode was found on chromosome 2 (SS2). Also, QTL affecting average daily gain (ADC), was identified to be expressed with Mendelian express mode.

• Molecules and Cells
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• v.25 no.3
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• pp.407-416
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• 2008

Thirteen near-isogenic lines (NILs) of japonica rice were developed via a backcross method using the recurrent parent Chucheong, which is of good eating quality but is susceptible to Magnaporthe grisea, and three blast resistant japonica donors, Seolak, Daeseong and Bongkwang. The agro-morphological traits of these NILs, such as heading date, culm length, and panicle length, were similar to those of Chucheong. In a genome-wide scan using 158 SSR markers, chromosome segments of Chucheong were identified in most polymorphic regions of the 13 NIL plants, and only a few chromosome segments were found to have been substituted by donor alleles. The genetic similarities of the 13 NILs to the recurrent parent Chucheong averaged 0.961, with a range of 0.932-0.984. Analysis of 13 major blast resistance (R) genes in these lines using specific DNA markers showed that each NIL appeared to contain some combination of the four R genes, Pib, Pii, Pik-m and Pita-2, with the first three genes being present in each line. Screening of nine M. grisea isolates revealed that one NIL M7 was resistant to all nine isolates; the remaining NILs were each resistant to between three and seven isolates, except for NIL M106, which was resistant to only two isolates. In a blast nursery experiment, all the NILs proved to be more resistant than Chucheong. These newly developed NILs have potential as commercial rice varieties because of their increased resistance to M. grisea combined with the desirable agronomic traits of Chucheong. They also provide material for studying the genetic basis of blast resistance.