水稻产量相关QTL研究现状

产量是最为复杂的数量性状,对它的遗传机理了解甚微。近15年来,许多学者利用随机分离群体定位了许多影响水稻产量及其组分的QTL,即以QTL定位的方法对产量潜力进行遗传剖析。试验证明上位性效应对产量及其组分性状遗传变异起着重要作用,但目前大多数QTL研究仍侧重于发掘和克隆单个主效QTL,然而对单一基因／QTL的深入了解还不足以诠释复杂性状遗传基础的全貌,还没有为育种家提供足够的可应用于分子标记辅助育种的遗传信息并用于提高水稻产量。笔者认为今后的数量性状研究尚需加强复杂性状QTL遗传网络的发掘,在改良水稻品种性状的同时发展并完善QTL研究。     

水稻QTL分析的研究进展

水稻许多重要的性状是由多基因控制的数量性状,经典的数量遗传学只能把数量性状作为一个整体进行研究。近年来．高密度分子标记连锁图的构建和有效的生物统计学方法的发展使人们对数量性状遗传基础的研究出现了革命性的变化。通过对不同群体内的个体或品系的分子标记基因型和表型数据的共分离分析,能对QTL进行检测和定位。本文对QTL定位的原理和方法进行了介绍,从QTL的数目和效应、上位性效应、QTL基因型与环境的互作、相关性状的QTL以及个体发育不同阶段的QTL等方面对水稻QTL分析的研究进展进行了综述。水稻基因组测序计划已经完成,本文还对基因组时代水稻QTL精细定位和克隆的方法进行了探讨,对QTL分析在水稻育种中的应用前景进行了展望。     

Toward understanding genetic mechanisms of complex traits in rice

Rice is the primary carbohydrate staple cereal feeding the world population. Many genes, known as quantitative trait loci (QTLs), con-trol most of the agronomically important traits in rice. The identification of QTLs controlling agricultural traits is vital to increase yield and meet the needs of the increasing human population, but the progress met with challenges due to complex QTL inheritance. To date,many QTLs have been detected in rice, including those responsible for yield and grain quality; salt, drought and submergence tolerance;disease and insect resistance; and nutrient utilization efficiency. Map-based cloning techniques have enabled scientists to successfully fine map and clone approximately seventeen QTLs for several traits. Additional in-depth functional analyses and characterizations of these genes will provide valuable assistance in rice molecular breeding.     

The genetic architecture of quantitative traits: lessons from Drosophila

Understanding the genetic architecture of quantitative traits begins with identifying the genes regulating these traits, mapping the subset of genetically varying quantitative trait loci (QTLs) in natural populations, and pinpointing the molecular polymorphisms defining QTL alleles. Studies in Drosophila have revealed large numbers of pleiotropic genes that interact epistatically to regulate quantitative traits, and large numbers of QTLs with sex-, environment- and genotype-specific effects. Multiple molecular polymorphisms in regulatory regions of candidate genes are often associated with variation for complex traits. These observations offer valuable lessons for understanding the genetic basis of variation for complex traits in other organisms, including humans.     

Identification, isolation and pyramiding of quantitative trait loci for rice breeding

Many agronomically important traits are governed by several genes known as quantitative trait loci (QTLs). The identification of important, QTL-controlled agricultural traits has been difficult because of their complex inheritance; however, completion of the rice genomic sequence has facilitated the cloning of QTLs and their pyramiding for breeding. Because QTLs are derived from natural variation, the use of a wider range of variations such as that found in wild species is important. In addition, Introgression Lines (ILs) developed from wild species in combination with Marker Assisted Selection should facilitate efficient gene identification. This review describes recent developments in rice QTL analysis including mapping, cloning and pyramiding QTLs.     

Yield-enhancing quantitative trait loci (QTLs) from wild species

Wild species of crop plants are increasingly being used to improve various agronomic traits including yield in cultivars. Dense molecular maps have enabled mapping of quantitative trait loci (QTLs) for complex traits such as yield. QTLs for increased yield have been identified from wild relatives of several crop plants. Advanced backcross QTL analysis has been used to identify naturally occurring favorable QTL alleles for yield and minimize the effect of unwanted alleles from wild species. Yield QTLs from wild species are distributed on almost all chromosomes but more often in some regions. Many QTLs for yield and related traits derived from different wild accessions or species map to identical chromosomal regions. QTLs for highly correlated yield associated traits are also often co-located implying linkage or pleiotropic effects. Many QTLs have been detected in more than one environment and in more than one genetic background. The overall direction of effect of some QTLs however, may vary with genetic context. Thus, there is evidence of stable and consistent major effect yield-enhancing QTLs derived from wild species in several crops. Such QTLs are good targets for use in marker assisted selection though their context-dependency is a major constraint. Literature on yield QTLs mapped from wild species is summarized with special reference to rice and tomato.     

Bayesian analysis for genetic architecture of dynamic traits

The dissection of the genetic architecture of quantitative traits, including the number and locations of quantitative trait loci (QTL) and their main and epistatic effects, has been an important topic in current QTL mapping. We extend the Bayesian model selection framework for mapping multiple epistatic QTL affecting continuous traits to dynamic traits in experimental crosses. The extension inherits the efficiency of Bayesian model selection and the flexibility of the Legendre polynomial model fitting to the change in genetic and environmental effects with time. We illustrate the proposed method by simultaneously detecting the main and epistatic QTLs for the growth of leaf age in a doubled-haploid population of rice. The behavior and performance of the method are also shown by computer simulation experiments. The results show that our method can more quickly identify interacting QTLs for dynamic traits in the models with many numbers of genetic effects, enhancing our understanding of genetic architecture for dynamic traits. Our proposed method can be treated as a general form of mapping QTL for continuous quantitative traits, being easier to extend to multiple traits and to a single trait with repeat records.     

淹水和干旱条件下水稻根系形成的QTLs及候选基因分析

为了研究不同水分条件下组成型根系性状和适应性根系性状的遗传机制,利用由IR64／Azucena发展的双单倍体（DH）群体分析了淹水和干旱条件下水稻幼苗种子根长（SRL）、不定根数（ARN）、总根干重（RW）及其对应的相对参数（干旱和淹水条件下根系性状的比值）的QTLs。淹水与干旱条件下检测到一个共同的种子根长QTL和一个共同的总根干重QTL。同时对前人发表的遗传群体定位的根系性状QTLs进行比较分析,检测到几个共同的根系性状QTLs。对与细胞伸长、分裂相关的候选基因进行了定位,其中4个细胞壁相关的ESTs（OsEXP2,OsEXP4,EXT和Xet）被定位在与不同水分条件下检测出的根系性状QTLs的相同区间。     

Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers

Huge efforts have been invested in the last two decades to dissect the genetic bases of complex traits including yields of many crop plants, through quantitative trait locus (QTL) analyses. However, almost all the studies were based on linkage maps constructed using low-throughput molecular markers, e.g. restriction fragment length polymorphisms (RFLPs) and simple sequence repeats (SSRs), thus are mostly of low density and not able to provide precise and complete information about the numbers and locations of the genes or QTLs controlling the traits. In this study, we constructed an ultra-high density genetic map based on high quality single nucleotide polymorphisms (SNPs) from low-coverage sequences of a recombinant inbred line (RIL) population of rice, generated using new sequencing technology. The quality of the map was assessed by validating the positions of several cloned genes including GS3 and GW5/qSW5, two major QTLs for grain length and grain width respectively, and OsC1, a qualitative trait locus for pigmentation. In all the cases the loci could be precisely resolved to the bins where the genes are located, indicating high quality and accuracy of the map. The SNP map was used to perform QTL analysis for yield and three yield-component traits, number of tillers per plant, number of grains per panicle and grain weight, using data from field trials conducted over years, in comparison to QTL mapping based on RFLPs/SSRs. The SNP map detected more QTLs especially for grain weight, with precise map locations, demonstrating advantages in detecting power and resolution relative to the RFLP/SSR map. Thus this study provided an example for ultra-high density map construction using sequencing technology. Moreover, the results obtained are helpful for understanding the genetic bases of the yield traits and for fine mapping and cloning of QTLs.     

Development and high-throughput genotyping of substitution lines carring the chromosome segments of indica 9311 in the background of japonica Nipponbare

Chromosome segment substitution lines (CSSLs) are useful for the precise mapping of quartitative trait loci (QTLs) and dissection of the genetic basis of complex traits.In this study,two whole-genome sequenced rice cultivars,the japonica Nipponbare and indica 9311 were used as recipient and dtonor,respectively.A population with 57 CSSLs was developed after crossing and back-crossing assisted by mo lecular rnarkers,and genotypes were identified using a high-throughput resequencing strategy,Detailed graphical genotypes of 38 lines were constructed based on resequencing data.These CSSLs had a total of 95 substituted segments derived from indica 9311,with an average of about 2.5 segments pet CSSL and eight segments per chromosome,and covered about 87.4％ of the rice whole genome.A multiple linear regression QTL analysis mapped four QTLs for 1000-grain weight.The largest-effect QTL was located in a region on chromosome 5 that contained a cloned major QTL GW5/qSW5 for grain size in rice.These CSSLs with a background of Nipponbare may provide powerful tools for future whole-genome discovery and functional study of essential genes/QTLs in rice,and offer ideal materials and foundations for japonica breeding.