Association Mapping of Quantitative Trait Loci for Grain Size in Introgression Line Derived from Oryza Rufipogon

Grain size is one of the critical agronomic traits governing grain yield and quality in rice. However, the underlying genetic mechanisms that control grain size in rice are poorly understood. We used an introgression line derived from Zhonghui 8015 and Oryza rufipogon Griff. This introgression line was evaluated under two different environmental conditions to dissect the quantitative trait loci controlling grain size. Genome-wide association study (GWAS) was performed using 28 193 SNPs through a general linear model, and 56 significant SNPs on different loci associated with the 4 grain size traits were detected. Cloned genes including GS3 and qGL3 showed substantial effects on grain length and size. Seven new stable loci were identified with pleiotropic effects on grain size. Haplotype, gene expression analyses, combined gene-based associations, and functional annotations permitted the shortlisting of important dominant genes including GS3 and qGL3.     

Genotype × Environment Interactions for Agronomic Traits of Rice Revealed by Association Mapping

Agronomic traits are important determinants to rice yield, which are controlled by complex genetic factors as well as genotype by environment(G×E) interaction effects. The G×E effects for agronomic traits of rice have been dissected with various approaches, but not with the current available approach, the association studies. In this study, a total of 32 655 single nucleotide polymorphisms were used to carry out associations with 14 agronomic traits among 20 rice accessions in two environments. The G×E interaction effects for all the agronomic traits were at highly significant levels(P 0.01), accounting for 3.4%–22.3% of the total sum of squares except for the length of brown rice. Twenty three putative quantitative trait loci(QTLs), including five previously known and several new promising associations, were identified for 10 of 14 traits. Analysis of the relationships between the traits for which QTLs and the genotype effects could be identified suggested that the higher the genotypic effect, the higher the possibility to identify QTLs for the given trait. The new QTLs detected in this study will facilitate dissection of the complex agronomic traits and may give insight into the G ×E effects with association mapping.     

Identification of quantitative trait loci controlling nodulation and shoot mass in progenies from two Brazilian soybean cultivars

Nitrogen (N) demand of soybean [Glycine max (L.) Merrill] can be supplied via biological nitrogen fixation (BNF), however, higher yielding cultivars increase plant demand for N. Phenotypes differing for traits associated with biological nitrogen fixation result from the expression of the multiple genes of both the host plant and the microsymbiont, but limited studies have been done on the genetics of the soybean BNF. Integrated maps of soybean with simple sequence repeat (SSR) markers [Cregan, P.B., Jarvik, T., Bush, A.L., Shoemaker, R.C., Lark, K.G., Kahler, A.L., Kaya, N., Van Toai, T.T., Lohnes, D.G., Chung, J., Specht, J.E., 1999. An integrated genetic linkage map of the soybean genome. Crop Sci. 39, 1464–1491.] offer an excellent opportunity for the identification of traits related to BNF. This study aimed at the identification of quantitative trait loci (QTLs) controlling BNF and nodulation in an F₂ population of 160 plants derived from an intraspecific cross between two Brazilian cultivars, Embrapa 20 × BRS 133, previously identified as having good potential for mapping of QTLs [Nicolás, M.F., Arias, C.A.A., Hungria, M., 2002. Genetics of nodulation and nitrogen fixation in Brazilian soybean cultivars. Biol. Fertil. Soils 36, 109–117.]. From 252 SSR markers tested in the parental genotypes 45 were polymorphic with high heterozygotes resolution. Mapping was performed with those 45 SSR markers for nodulation [nodule number (NN) and nodule dry weight (NDW)] and plant growth [shoot dry weight (SDW)] phenotypes in F_2:3 lines. A total of 21 SSR loci were mapped with a likehood of odds (LOD) value of 3.0 and a maximum Haldane distance of 50 cM, and were distributed in nine linkage groups with coverage of 251.2 cM. The interval mapping analysis with Mapmaker/QTL revealed two genomic regions associated with NN and NDW, with a contribution of putative QTLs of 7.1 and 10%, respectively. The regression analysis identified 13 significant associations between the marker loci and QTLs due to additive effects, with some of them being significantly associated with more than one phenotypic trait. Effects were observed in all variables studied, ranging from 2 to 9%. A one-way analysis of variance (ANOVA) also detected 13 significant associations, related to dominance effects. A two-way-ANOVA showed six epistatic interactions among non-linked QTLs for SDW, NN and NDW, explaining up to 15% of the trait variation and increasing the phenotypic expression from 8 to 28%. The data obtained in this work establish the initial stage for additional studies of the QTLs controlling BNF and indicate that effective marker-assisted selection using SSR markers may be feasible for enhancing BFN traits in soybean breeding programs.     

Application of Molecular Markers in Breeding for Nitrogen Use Efficiency

Summary

Nitrogen use efficiency (NUE) is defined as dry matter yield produced per unit of N supplied and available in the soil. NUE is approximately 33% for cereal production worldwide. Increased cereal NUE must accompany increased yield needed to feed the growing world population. Consequently, continued efforts are needed to include plant selection under low N input which is not often considered a priority by plant breeders. Molecular markers have accelerated plant breeding in a number of areas including biotic (disease and insect) resistance and abiotic (drought, low nitrogen fertilization and frost) tolerance. Marker-based technology has already provided scientists with a powerful approach for identifying and mapping quantitative trait loci (QTL) and would lead to the development of a better understanding of genetic phenomena. Two main NUE studies have been discussed. The first study identified QTL for NUE in maize involved the grain yield and secondary morphological traits of interest, such as plant height, ear leaf area, ears per plant and kernels per ear. This was compared with second study of QTL for yield and its components with genes encoding cytolistic gult-amine synthestase and leaf N0₃ ^- content. These secondary traits were correlated with yield and demonstrated segregation with high heritability under low nitrogen conditions. Marker assisted selection (MAS) should be able to offer significant advantages in cases where phenotypic screening is particularly expensive or difficult, including breeding projects involving multiple genes, recessive genes, late expression of the trait of interest, seasonal considerations, or geographical considerations. In addition to reducing costs of conventional breeding, MAS also has the potential to generate time savings. Possibly, the greatest contribution of QTL mapping to plant breeding will be the basic understanding of the genetic architecture of quantitative traits, thereby relating specific genetic loci with the biological mechanisms associated with desirable phenotypes.     

Identification of New Resistance Loci Against Sheath Blight Disease in Rice Through Genome-Wide Association Study

Sheath blight (SB) caused by the soil borne pathogen Rhizoctonia solani is one of the most serious global rice diseases. Breeding resistant cultivar is the most economical and effective strategy to control the disease. However, no rice varieties are completely resistant to SB, and only a few reliable quantitative trait loci (QTLs) linked with SB resistance have been identified to date. In this study, we conducted a genome-wide association study (GWAS) of SB resistance using 299 varieties from the rice diversity panel 1 (RDP1) that were genotyped using 44 000 high-density single nucleotide polymorphism (SNP) markers. Through artificial inoculation, we found that only 36.5% of the tested varieties displayed resistance or moderate resistance to SB. In particular, the aromatic and aus sub-populations displayed higher SB resistance than the tropical japonica (TRJ), indica and temperate japonica sub-populations. Seven varieties showed similar resistance levels to the resistant control YSBR1. GWAS identified at least 11 SNP loci significantly associated with SB resistance in the three independent trials, leading to the identification of two reliable QTLs, qSB-3 and qSB-6, on chromosomes 3 and 6. Using favorable alleles or haplotypes of significantly associated SNP loci, we estimated that both QTLs had obvious effects on reducing SB disease severity and can be used for enhancing SB resistance, especially in improving SB resistance of TRJ sub-population rice varieties. These results provided important information and genetic materials for developing SB resistant varieties through breeding.     

Association mapping in rice: basic concepts and perspectives for molecular breeding

In the last decade, association mapping (AM) has become a well-established method to detect genes and quantitative trait loci (QTLs) associated with agronomically important traits. The identification of a large number of single nucleotide polymorphisms (SNPs) from genome sequencing and concurrent development of high-throughput genotyping platforms has led to AM being widely used for a range of crops. These technologies have been used in rice (Oryza sativa) to explore the abundant diversity and there is enormous potential to identify novel QTLs for traits of interest. Due to the availability of cost-effective high-throughput SNP genotyping methods and rapid developments in rice genomics, it is inevitable that these AM approaches will become more popular in the future, especially in the context of genome-wide association studies (GWASs). In this paper, we review the fundamental concepts, critical considerations and limitations of AM focusing on rice, and reiterate the importance of accurate phenotypic data. We also include a section about connecting GWAS to molecular breeding, covering practical consideration for breeders, which is required to use GWAS results in actual rice molecular breeding programs and which has not received adequate attention in the scientific literature.     

Localization,validation and characterization of plant-type QTLs on chromosomes 4 and 6 in rice (Oryza sativa L.)

Improvement of rice (Oryza sativa L.) plant type is a major breeding objective. This study aimed to precisely localize and characterize key genomic regions for plant type using near-isogenic individuals. Selfing of partially heterozygous F₅ recombinant inbred (RI) individuals [parental varieties Milyang 23 (M23) and Akihikari (AK)] developed heterogeneous inbred families (HIFs) composed of 108 and 93 F₇ progenies, which segregated at molecular marker loci on the long arms of chromosomes 4 and 6, respectively. The progeny lines (F₈) were evaluated for traits composing plant type in Los Baños, Philippines, to locate quantitative trait loci (QTLs) using interval mapping and to evaluate the effects of the QTL region by phenotypic comparison between the genotypes. QTLs for the traits were detected in 17 cM across XNpb12 on chromosome 6. The M23 homozygote for the QTL region resulted in a >7% increase and decrease in plant length and tiller number at heading, respectively, relative to the AK homozygote. Consequently, culm length (CL) and traits determining flag-leaf and panicle sizes increased 5–56% by the M23 homozygote, together with a 15% decrease in panicle number. For a QTL region detected in 6 cM across XNpb235 on chromosome 4, the AK homozygote had similar effects on these traits, except CL. The directions and magnitudes of their effects agreed with those previously estimated in the RI line population, thus increasing confidence in primary QTL analyses for plant type. Analyzing the HIFs validated and characterized the two QTL regions greatly involved in determining varietal plant type from an early growth stage to maturity, providing information useful for empirical and marker-assisted breeding towards rice improvement.     

Upland rice grown in soil-filled chambers and exposed to contrasting water-deficit regimes: II. Mapping quantitative trait loci for root morphology and distribution

Root morphological characteristics are known to be important in the drought resistance of some rice (Oryza sativa L.) varieties. The identification of quantitative trait loci (QTLs) associated with root morphology and other drought resistance-related traits should help breeders produce more drought resistant varieties. Stability in the expression of root growth QTL across rooting environments is critical for their use in breeding programs. A greenhouse experiment in which a mapping population of 140 recombinant inbred lines and the parental varieties Bala and Azucena were grown in glass-sided soil chambers and evaluated for root growth and water uptake was conducted. In each of 2 years, two treatments were used; an early water-deficit (WD0) in which seeds were sown into wet soil but received no more water, and a late water-deficit (WD49) in which the plants were watered for 49 days and then received no water for a week. The major differences between treatments and years in dry matter partitioning and root growth traits are reported elsewhere. Here, the identification of QTLs for root growth traits by composite interval mapping is described. At LOD>3.2, there were six QTLs for the weight of roots below 90 cm and maximum root length, 11 for root to shoot ratio, 12 for the number of roots past 100 cm, and 14 for root thickness. A total of 24 regions were identified as containing QTLs (these regions often contained several QTLs identified for different root traits). Some were revealed only in individual experiments and/or for individual traits, while others were common to different traits or experiments. Seven QTLs, on chromosomes 1, 2, 4, 7, 9 (two QTLs) and 11, where considered particularly noteworthy. The complex results are discussed in the context of previously reported QTLs for root growth in other populations, the interaction between QTL with the environment and the value of QTLs for breeding.     

Fine Mapping of QTLs for Stigma Exsertion Rate from Oryza glaberrima by Chromosome Segment Substitution

Stigma exsertion is an important trait for outcrossing ability in rice. Stigma exsertion rate (SER) of male sterile lines (MSLs) is a key factor affecting F₁-seed production in hybrid rice. In this study, seven QTLs for SER were detected on five chromosomes using a set of single-segment substitution lines (SSSLs) derived from O. glaberrima. Three of the QTLs were mapped in the estimated intervals of 92.5–333.0 kb. qSER-5 was located in a substitution segment of 92.5 kb. qSER-1b and qSER-8b were respectively limited to 333.0 kb and 107.5 kb by secondary substitution mapping. qSER-1b and qSER-3 had bigger additive effects of 11.5% and 11.9%, respectively, while the other five QTLs had smaller additive effects from 5.7% to 8.6%. Open reading frames were identified in the regions of qSER-5 and qSER-8b in O. sativa and O. glaberrima genomes. Fine mapping of the QTLs laid a foundation for the cloning of genes, and QTLs for SER will be used to develop MSLs with strong ability of outcrossing.     

Rapid prediction of head rice yield and grain shape for genome-wide association study in indica rice

Rice milling and appearance qualities are the main determinants of market price of the milled rice, so great breeding efforts have been directed to improve the milling and appearance quality. The success of breeding efforts depends on the accurate and rapid phenotyping of the quality traits in early generations. This study was conducted to first validate the effectiveness of the PaddyCheck to measure head rice yield (HRY) and paddy grain length of 40 indica rice cultivars. The results indicated that the PaddyCheck data had positively correlated with the lab methods of HRY (r = 0.81**) and grain length (r = 0.97**). An association panel including 281 indica rice accessions was phenotyped with the PaddyCheck and the data were used for genome-wide association study (GWAS) to identify quantitative trait locus (QTL) for milling and appearance quality. A total of nine QTLs were identified, among which the major genes GS3 and qSW5 were identified for grain length and width, respectively. Furthermore, a novel QTL on short arm of chromosome 6 was identified for HRY. Our study indicated that PaddyCheck measurement was accurate and effective, and could be applied in rice breeding for improvement of grain shape and milling quality. The nine QTLs identified in indica rice could be used in marker assisted selection in rice breeding programs.     

Quantitative Trait Loci for Heading Date and Their Relationship with Genetic Control of Yield Traits in Rice (Oryza sativa)

Grain yield and heading date are key factors determining the commercial potential of a rice variety. Mapping of quantitative trait loci (QTLs) in rice has been advanced from primary mapping to gene cloning, and heading date and yield traits have always attracted the greatest attention. In this review, genomic distribution of QTLs for heading date detected in populations derived from intra-specific crosses of Asian cultivated rice (Oryza sativa) was summarized, and their relationship with the genetic control of yield traits was analyzed. The information could be useful in the identification of QTLs for heading date and yield traits that are promising for the improvement of rice varieties.     

冰草10个主要农艺性状的QTL定位研究

为了给冰草分子标记辅助育种提供依据,以蒙古冰草、航道冰草及其F2群体为试验材料,在已构建的冰草分子连锁遗传图谱的基础上采用多QTL模型法对茎粗、叶长、叶宽、分蘖数、茎叶比、叶片数、小穗长、单株鲜重、单株干重等10个主要农艺性状进行了QTL定位分析.试验共检测到13个QTL,分布在1、2、3、4、5、7共6个连锁群上,其加性效应各不相同,遗传贡献率变化范围为10.1％～33.9％.在13个QTL中,有1个与株高相关QTL、1个叶长相关QTL,1个单株鲜重相关QTL,2个单株干重相关QTL,1个叶宽相关QTL,1个分蘖数相关QTL,2个茎粗相关QTL,1个叶片数相关QTL,2个茎叶比相关QTL,1个穗长相关QTL.     

Genetic control of processing quality in a bread wheat mapping population grown in water-limited environments

End-use quality of bread wheat (Triticum aestivum L.) is affected by both genetic and environmental variation. Current understanding of the genetic control of wheat quality traits is mainly based on genetic experiments conducted using grain produced in favourable conditions. The objective of this research was to extend the genetic analysis of these traits by using grain produced in water-limited environments. Grain samples harvested from a mapping population grown in field experiments at two locations in Australia were used to assess characteristics of the grain, flour, dough and bread. Quantitative trait loci (QTLs) were mapped. The parents of the population, RAC875 and Kukri, differ at several loci that are known to affect grain quality or plant phenology. Of these, a high-molecular-weight glutenin locus (Glu-B1) affected dough properties, the puroindoline-encoding Ha locus affected grain hardness, flour and loaf properties and a photoperiod response locus (Ppd-D1) affected flour extraction and protein content. Similarly, several previously reported quantitative trait loci (not associated with specific genes) also had effects in the stress environments used here. In addition, novel loci were detected for bread wheat quality traits; their effects may be specific to materials grown in water-limited environments.     

New Stably Expressed Loci Responsible for Panicle Angle Trait in Japonica Rice in Four Environments

Panicle angle (PA) of 254 recombinant inbred lines derived from a cross between two japonica varieties Xiushui 79 and C Bao was investigated under four environments,and a genetic linkage map including 111 SSR markers was constructed.Genetic analysis was conducted by mixed major gene plus polygene inheritance models,and quantitative trait loci (QTLs) identification by the QTLNetwork 2.0 and the composite interval mapping approach of WinQTLCart 2.5 software.Results showed that the PA trait was controlled by two major genes plus polygenes,mainly by major genes.Eight QTLs for PA were detected by the QTLNetwork 2.0 software,and each locus explained 0.01% to 39.89% of the phenotypic variation.Twelve QTLs for PA were detected by the WinQTLCart 2.5 software,with each locus explaining 2.83% to 30.60% of the phenotypic variation.Two major QTLs (qPA9.2 and qPA9.5) distributed between RM3700 and RM3600 and between RM5652 and RM410,respectively,and a moderate QTL (qPA9.7) distributed between RM257 and OSR28,were both detected by the two methods in all of the four environments.The negative effect alleles of the three QTLs were from Xiushui 79.In addition,eight pairs of epistatic QTLs with minor effects were also detected.QTL × environment interactions were not significant for additive QTLs and epistatic QTL pairs.     

Marker-assisted genetic analysis of non-acclimated freezing tolerance and cold acclimation capacity in a backcrossSolarium population

Random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers were used to construct a partial genetic linkage map in a potato backcross population. The population, derived from two diploid wildSolatium species (frost tolerant, able to cold acclimateS. commersonii; frost sensitive, unable to cold acclimateS. cardiophyllum), was used to map quantitative trait loci (QTL) of non-acclimated relative freezing tolerance (NARFT) and cold acclimation capacity (CAC). Precise assessment of these traits allowed distinction of small but significant differences among 35 backcross genotypes. NARFT and CAC were not correlated in the segregating population, suggesting independent genetic control for these two major components of freezing tolerance. The linkage map spanned 479.4 cM and included 77 RAPD markers and two SSR markers, with 38 RAPD and 10 SSR unassigned markers. Two QTLs for NARFT were detected in two different linkage groups, accounting for 44.0% of the phenotypic variation for this trait. Two QTLs for CAC were detected, accounting for 24.9% of the phenotypic variation for this trait. QTLs for NARFT and CAC were detected at separate genomic regions, in support of the independent genetic control of these two traits. QTLs for NARFT and CAC were detected in a linkage group identified as part of chromosome V, suggesting that such chromosome constitutes a prime candidate for fine-mapping. Due to the relatively small progeny size evaluated in this study, additional QTLs for NARFT and CAC could have been involved but not identified. Therefore, the conclusions derived from this study should be considered preliminary.     

QTL Analysis for Grain Iron and Zinc Concentrations in Two O. nivara Derived Backcross Populations

Identification of quantitative trait loci (QTLs) for grain mineral elements can assist in faster and more precise development of micronutrient dense rice varieties through marker-assisted breeding. In the present study, QTLs were mapped for Fe and Zn concentrations in two BC₂F₃ mapping populations derived from the crosses of O. sativa cv Swarna with two different accessions of O. nivara. In all, 10 and 8 QTLs were identified for grain Fe and Zn concentrations in population 1, and 7 and 5 QTLs were identified in population 2, respectively. Eighty percent of the QTLs detected in both populations were derived from O. nivara. Five QTLs for Fe and three QTLs for Zn explained more than 15% phenotypic variance either in interval or composite interval mapping. The locations of O. nivara derived QTLs such as qFe2.1, qFe3.1, qFe8.2 and qZn12.1 were consistently identified in both the populations. Epistatic interaction was observed only between RM106 and RM6 on chromosome 2 and between RM22 and RM7 on chromosome 3 for Fe concentration in population 1. Sixteen candidate genes for metal homeostasis were found to co-locate with 10 QTLs for Fe and Zn concentrations in both the populations. Most of the Fe and Zn QTLs were found to co-locate with QTLs for grain yield and grain quality traits. Some of the major effect QTLs identified can be used to improve rice grain Fe and Zn concentrations.     

The genetic control of grain protein content variation in a doubled haploid population derived from a cross between Australian and North American two-rowed barley lines

Grain protein content (GPC) is a major determinant of malting quality in barley, as it influences many aspects of the malting and brewing processes. The objective of the present study was to apply a quantitative trait loci (QTL) mapping approach towards a dissection of the genetic factors involved in phenotypic trait expression. The mapping population comprised 180 doubled haploid lines derived from a cross of parents (VB9524 and ND11231*12) with inherently low GPC. These lines were grown at eight environments in Australia and North Dakota, USA, between 2000 and 2002 and measured for GPC, grain yield, plant height and heading date. QTL analyses with a linkage map of 211 markers identified seven loci significantly (LOD>3.6) linked to variations in GPC. Collectively, these loci accounted for approximately 74% of the total genetic variance for GPC in the population, that is, after adjusting for QTL×environment interactions (QTL×E). QTL×E was highly (P<0.001) significant, but was largely due to differences in magnitude of QTL effects rather than changes in the direction of the effects. Of the seven identified QTLs, five were located at intervals adjacent to those for other agronomic traits, leading to the suggestion that genotype–environment interactions for GPC may also involve pleiotropic or linkage interactions with genes responsible for variation in these traits.     

Improvement of Rice Resistance to Sheath Blight by Pyramiding QTLs Conditioning Disease Resistance and Tiller Angle

Rice resistance to sheath blight （SB） is controlled by polygenes or quantitative trait loci （QTLs） and affected by plant morphological traits, qSB-9^TQ and TAG1^TQ, which control SB resistance and tiller angle （TA）, respectively, were employed to test whether the combination of the two genes will further improve rice SB resistance and reduce yield loss rather than only one of them or neither. Using two pairs of near isogenic lines （NILs）, TAC1^TQ was confirmed to contribute to SB resistance. However, its effect was less considerable than that of qSB-9^TQ. Subsequently, the two genes were introduced into two commercial rice varieties to develop a series of NILs. The NILs carrying both TAG1^TQ and qSB-9^TQ showed more resistance than the NILs containing only one of them. Comparing the grain yield per plant （GYP） under the three different SB disease conditions, namely slight, moderate and severe conditions, NILs carrying both genes apparently lost lower GYP than the NILs without the two genes and the NILs carrying only TAC1^TQ. Under slight disease condition, no significant differences were found on morphology, development and GYP associated traits except for TA between the NILs carrying both genes and either of them, indicating that the two genes have no inferior effect on rice agronomic traits. Results indicated that mAC1^TQ and qSB-9^TQ have high breeding potential, and pyramiding SB resistance QTL and morphological trait QTL is a potential approach in improving rice SB resistance.     

Polygene mapping as a tool to study the physiology of potato tuberization and dormancy

Efforts to breed for the ability to tuberize under long days or for the length of tuber dormancy should benefit not only from information on the location of genes associated with these traits, but also from an understanding of the hormones the genes control. Understanding the role of the respective genes is a logical step in developing the best breeding strategy, both for conventional breeding and for gene transfer using molecular techniques. Polygene mapping affords a way to achieve such understanding and is also a tool to study the physiology of potato tuberization and potato tuber dormancy. The addition of DNA markers to a plant population facilitates the mapping of polygenes that control quantitatively inherited traits segregating in the population. A quantitative trait locus denotes a region of chromosome that is linked to the marker gene and which has a significant effect on the quantitative trait under study. Our approach has been to find the quantitative trait loci associated with tuberization and tuber dormancy in a segregating diploid population, and then to map the population for quantitative trait loci associated with levels of hormones implicated in the control of these two traits. We are using a population derived from a hybrid between haploidSolanum tuberosum andS. berthaultii that was backcrossed to a different haploidS. tuberosum. We have found ten quantitative trait loci for the ability to tuberize under long days and eight quantitative trait loci for tuber dormancy. In the same population we have found one or more quantitative trait loci for polyamines, abscisic acid, tuberonic acid, tuberonic acid glucoside, zeatin riboside, and gibberellin A₁. Some of the hormone quantitative trait loci have coincided with quantitative trait loci for tuberization or dormancy. Implications of such commonality are discussed, along with the usefulness and limitations of the methods.     

Genetic dissection of grain nitrogen use efficiency and grain yield and their relationship in rice

Breeding for improved grain yield (GY) and grain nitrogen use efficiency (NUE) is an important objective of many rice breeding programs. A better understanding of the genetics of these two complex traits and their genetic relationship is required for more efficient breeding. This study reports the results of a linkage mapping study conducted for these two traits using 127 rice recombinant inbred lines (RILs) derived from the cross of Zhanshan 97/Minghui 63. Phenotypic data were collected under two nitrogen conditions in 2006 and 2007. For NUE, four and six QTLs were identified in 2006 and 2007, respectively. These QTLs were on chromosomes 1, 2, 6, 7 and 11. For GY, nine and five QTLs were detected on chromosomes 1, 2, 7 and 11 in 2006 and 2007, respectively. The phenotypic and genetic correlations between NUE and GY are positive and highly significant. Four genomic regions, including C86-C2340 on chromosome 1, RZ599-R1738 on chromosome 2, RZ471-C1023 on chromosome 7 and R3203-RM20a on chromosome 11, were found to contain QTLs for both NUE and GY. The effects of the co-located QTLs were in the same direction for NUE and GY, providing a genetic basis for the observed positive genetic correlation between the two traits. These genomic regions might be explored for the simultaneous improvement of NUE and GY in breeding.