rice is the main food resource worldwide and the staple food in korea . with the advent of a new hybridization technique in the late 1960s , the  tongil 
variety was developed by setting up a cross between indica and japonica rice varieties ; up to the 1980s , this variety produced sufficient yield to meet the requirements of south korea . at present , improved japonica varieties are usually cultivated , and the  tongil  type varieties are only occasionally cultivated for processing and special purposes . since the 1980s , the demand for high - quality rice has increased due to the diverse requirements of consumers . therefore ,
improving the chemical composition and physical characteristics of rice is essential for developing rice varieties according to the preference of consumers and having health benefits as well as good quality .
rice quality parameters such as the appearance , nutrition value , and taste and texture of cooked rice , color , and whole kernel morphology are important factors that affect consumer preferences . in addition , the major chemical components , that is , carbohydrates ( 7275% ) , proteins ( 710% ) , and lipids ( 1% ) , are important factors that reflect the nutritional aspect of rice ; the structure and compositions of the proteins and fatty acids are also important parameters .
for cooked rice , texture and odor are important factors that determine the quality . in particular ,
texture is affected by the degree of solidity , adhesion , and cohesion ; the ratio of amylose to amylopectin can also affect the texture of cooked rice .
although there are no methods to evaluate objectively the taste because it is a subjective parameter , taste is an important factor to evaluate the quality of rice .
odor is also one of the important factors that affect the taste of cooked rice .
the period for which rice is stored after harvest can affect the aroma of cooked rice irrespective of the varieties .
rice that tastes good after cooking is known to have less than 7% protein and 15.516.5% water content .
rice with high protein content is hard , less elastic , and less viscous after being cooked .
in addition , the unsaturated fatty acid content of rice determines the appearance and quality of cooked rice grains [ 2 , 3 ] .
the crude fatty acid contents of rice include palmitic acid , oleic acid , and linoleic acid .
usually , rice with a high content of lipids is considered unhealthy ; however , if the fat content mostly comprises unsaturated fatty acids , the health risks are low .
the qtls related to amylose , protein , and fat content were detected in previous researches .
the qtls related to amylose and fat content , amy1 on chromosome 7 and amy2 on chromosome 8 with 20.4% of phenotypic variation and fat1 on chromosome 7 with 7.2% of variation , are detected from recombinant inbred lines ( rils ) population .
six of qtls related to amylose content and five qtls for protein content were detected on chromosomes 2 and 12 .
also rice protein content ( rpc ) and rice fat content ( rfc ) were identified from doubled haploid population including two rpc qtls ( qrpc-5 , qrpc-7 ) and two rfc qtls ( qrfc-2 , qrfc-5 ) .
eight qtls , three qtls , and six qtls associated with protein , amylose , and fatty acid , respectively , were detected from rils population in three different locations which are wonju , daegu , and iksan of korea .
five qtls for protein content ( pc ) were detected on chromosomes 3 , 4 , 5 , 6 , and 10 , respectively .
a major qtl qpc-6 was located near the wx marker rm190 on the short arm of rice chromosome 6 , explaining 19.3% of the phenotypic variance and showing an additive effect of 0.471% .
the other four qtls explained 3.910.5% of the phenotypic variance and had additive effects of 0.2130.343% .
four qtls for fat content ( fc ) were detected on chromosomes 3 , 5 , 6 , and 8 , respectively . among these loci ,
qfc-5 on chromosome 5 was the qtl with the largest effect , explaining 12.9% of the phenotypic variance and showing an additive effect of 0.091% .
qtl related to rice lipid content ( rlc ) with 2.37 of lod score was identified on chromosome 5 from the high lipid mutant line derived from  dongjin  by t - dna insertion . in this study
, we investigated the growth characteristics and physicochemical properties of a  cheongcheong    nagdong  double haploid ( cndh ) population and performed the analysis of qtl to attempt to determine quantitative trait loci ( qtls ) associated with the taste of cooked rice and breed a new variety that produces rice having good taste .
a dh population consisting of 133 lines derived from a cross between  cheongcheong  and  nagdong  was cultivated by the institute of crop breeding , college of agriculture and biosciences , kyungpook national university , at an experimental field of the kyungpook national university , gunwi - gun , between 2010 and 2012 .
the plant materials were sown on april 20 , 2012 , and transplanted by planting density of 30  15  cm with one plant per each line on may 20 , 2012 .
all the cndh lines were planted with their parents with plants of only one line per planting row , and the planting density was 30  15  cm .
the amount of fertilizer applied was n  :  p2o5  :  k2o = 9.0  :  4.5  :  5.7  kg/10  a. phosphate and potassium were used as the main fertilizers , whereas nitric fertilizer was 70% of the main fertilizer used , and 30% of the topdressing fertilizer was used at the tillering stage .
herbicides and insecticides for preventing diseases and pests were used as per the standard cultivation method of rice ( the rural development administration , 2000 ) . excluding the plants of the lines that showed remarkable sterility and separating lines , 70 cndh lines were used to determine the qtls associated with the quality of cooked rice .
the growth characteristics of rice plants cultivated at the experimental field of kyungpook national university , gunwi , in 2012 , were investigated .
the following growth characteristics of 5 plants of each line were measured : plant height , length of panicles , the number of spikelets per panicle , and percentage of fertile grains .
the amylose , lipid , protein , and starch contents of rice were analyzed using near infrared spectroscopy ( nirs ) , and the crude fat with fatty acid content was determined by the bio - farming and functional materials for foods regional innovation center at the kyungpook national university , sangju campus .
nirs ( foss nirsystems 6500 ; usa ) was performed three times after damaged and broken grains and green and red kernels were removed .
qtls associated with rice quality were analyzed using 217 simple sequence repeat ( ssr ) markers obtained from the department of functional crop in rural development administration .
the winqtl cartographer ( winqtlcart , version 2.5 ) was used for the qtl analysis .
the composite interval mapping ( cim ) was used for whole genome scanning to detect qtls by using winqtlcart 2.5 at a threshold log of odds ( lod ) of 2.5 .
the qtl analysis was performed after the cndh population was cultivated with their parents ,  cheongcheong  and  nagdong  for 3 weeks in a green house .
our growth characteristic analysis revealed that the plant height of the cndh population was lower than that of the parents .
panicle length of the cndh population was lower than that of  cheongcheong  and higher than that of  nagdong .
 the number of spikelets per panicle , 1,000 grain weight , and yield of the cndh population were lower than those of  cheongcheong  and  nagdong  ( see supplementary table 1 in supplementary material available online at http://dx.doi.org/10.1155/2014/781832 ) ; these parameters showed continuous variation in cndh , suggesting a normal distribution ( figure 1 ) .
therefore , we analyzed the components of unpolished rice from the cndh population by using nirs .
the amylose content of  cheongcheong  is lower than  nagdong  while the protein and lipid content of  cheongcheong  is higher than  nagdong  ( table 1 ) .
thus , the correlation analysis revealed that the balance of the three components , amylose , protein , and lipid , is associated with the quality of rice ( table 2 ) .
the major 3 factors associated with the taste of cooked rice are generally known as amylose , protein , and lipid .
thus we performed the correlation analysis among these 3 factors in two consecutive years , 2012 and 2013 ( table 2 ) .
as shown in table 2 , protein and lipid were significantly different from amylose suggesting that lipid was relatively higher impact factor for determining rice taste .
however , in 2013 the factor of protein only seems to be significantly involved in the taste of cooked rice .
this slight difference might be due to the differential environmental condition from two consecutive years .
also , the frequency distribution of the three components in the cndh population showed a similar normal distribution except the frequency distribution in lipid content ( figure 2 ) .
the qtls related to amylose content were qamy-7 , qamy-11 - 1 , qamy-11 - 2 , and qamy-11 - 3 and that related to protein content was qpro-2 .
four of the qtls associated with amylose content were detected on chromosomes 7 and 11 .
rm6776-rm21105 on chromosome 7 had a log of odds ( lod ) score of 6.25 .
rm26771-rm26981 , rm26981-rm27242 , and rm25971-rm27123 on chromosome 11 had lod scores of 2.96 , 2.58 , and 3.59 , respectively .
the one qtl associated with protein content was detected on chromosome 2 ; rm12532-rm555 had lod scores of 4.88 .
further , one of the qtls associated with lipid content was detected on rm15064-rm15448 of chromosome 3 with an lod score of 3.55 ( table 3 , figure 3 ) .
the index of coincidence for the qtls related to amylose content was 70% for rm21105 on chromosome 7 ( supplementary table 2 ) and 80 , 75 , and 70% for rm26771 , rm3482 , and rm26801 ( supplementary table 3 ) , respectively .
the index of coincidence for the qtls related to protein content was 70% for rm12532 and rm555 on chromosome 2 and 75 , 75 , and 70% for rm506 , rm22198 , and rm22334 on chromosome 8 , respectively ( supplementary table 4 ) .
the index of coincidence for the qtls related to lipid content was 70% each for rm15063 and rm15448 ( supplementary table 5 ) on chromosome 3 .
we investigated the growth characteristics and analyzed the physicochemical properties of a doubled haploid population derived from a cross between  cheongcheong  and  nagdong  ( cndh ) to breed a rice variety that tastes good after cooking and to detect quantitative trait loci ( qtls ) associated with the taste of cooked rice .
the results suggest that the plant height , panicle length , number of spikelets per panicle , 1,000 grain weight , and yield of the cndh population show a normal distribution .
we further analyzed the contents of amylose , protein , and fatty acids in the rice grains .
correlation analysis of the amylose , protein , and lipid contents indicated that each compound is related to the taste of cooked rice .
in particular , the correlation coefficient of protein to amylose was significant at the level of 0.280 .
the advent of molecular markers has helped to facilitate the understanding of the genetic behavior of complex quantitative traits . doubled haploid population derived from 
ir64  indica type and  azucena  japonica type is exploited for analysis of qtl related to rice quality .
this study investigated the growth characteristics and analyzed the physicochemical properties of a doubled haploid population derived from a cross between  cheongcheong  and  nagdong  ( cndh ) to breed a rice variety that tastes good after cooking and detect quantitative trait loci ( qtls ) associated with the taste of cooked rice .
because of these advantages , diverse methods such as the development of an automated system by using the nirs program were attempted to evaluate the taste of cooked rice in developed countries . despite remarkable development of measurement technology , several factors can affect the result of measurement . in the distribution histogram ,
the components are not perfect normal distribution because of damage or changing in the content of amylose , protein , and lipid by period and method of harvest , drying , heat , period of storage , and moisture .
for determining amylose content and cohesion , alkali digestion value , and protein content , the basic physicochemical characteristics of rice measurement of the changes in amylogram characteristics yield more accurate results [ 13 , 14 ] .
the lower the amylose content , the higher the viscosity of cooked rice . in contrast , the viscosity of cooked rice is low when the amylose content is high because amylose captures amylopectin and inhibits the swelling of starch particles .
also , protein content decreases the taste of cooked rice because a layer of protein develops around the starch particles , reducing the viscosity and elasticity of cooked rice and directly affecting the gelatinization characteristics of starch .
the amylose contents between two parental cultivars were shown to be significantly different ( table 1 ) suggesting differential gene expression of waxy gene , one of the key regulators determining amylose content .
thus , as expected , intermediated extent of amylose content was detected in the hybrid of cheongcheong  nagdong double haploid ( cndh ) population .
although the smaller amounts of lipids are present in rice than the other components , they are a mediator of heat transfer and impart flavor .
lipids have emulsification characteristics and combine with proteins , thereby affecting the properties of matter in tissues .
the qtls related to amylose content were qamy-7 , qamy-11 - 1 , qamy-11 - 2 , and qamy-11 - 3 and those related to protein content were qpro-2 and qpro-8 .
four of the qtls associated with amylose content were detected on chromosomes 7 and 11 .
the index of coincidence for the qtls related to amylose content was 70% for rm21105 on chromosome 7 and 80 , 75 , and 70% for rm26771 , rm3482 , and rm26801 , respectively .
the index of coincidence for the qtls related to protein content was 70% for rm12532 and rm555 on chromosome 2 and 75 , 75 , and 70% for rm506 , rm22198 , and rm22334 on chromosome 8 , respectively .
the index of coincidence for the qtls related to lipid content was 70% each for rm15063 and rm15448 on chromosome 3 .
the qtls for amylose content were detected on chromosomes 3 , 6 , and 7 commonly [ 4 , 7 , 11 ] .
the qtls for protein content were detected commonly on chromosomes 3 , 6 , and 7 [ 68 ] .
also the qtls for lipid content were commonly detected on chromosomes 5 , 6 , and 7 [ 69 ] . in spite of many results , several new qtls related to amylose and
therefore , we can exploit several ssr markers on chromosomes 11 and 2 showing high coincidence ratio between genotype and phenotype .
the markers can be useful to select desirable lines for rice breeding and facilitate further research .
 we investigated the growth characteristics and analyzed the physicochemical properties of a doubled haploid population derived from a cross between  cheongcheong  and  nagdong  to breed a rice variety that tastes good after cooking and to detect quantitative trait loci ( qtls ) associated with the taste of cooked rice . 
 the results showed that these compounds also represent a normal distribution . 
 correlation analysis of the amylose , protein , and lipid contents indicated that each compound is related to the taste of cooked rice . 
 the qtls related to amylose content were 4  qtls , protein content was 2  qtls , and lipid content was 2  qtls . 
 four of the qtls associated with amylose content were detected on chromosomes 7 and 11 . 
 the index of coincidence for the qtls related to amylose , protein , and lipid content was 70% , respectively . 
 these markers showing high percentage of coincidence can be useful to select desirable lines for rice breeding . 
1. Introduction
2. Materials and Methods
3. Results
4. Discussion