Quantitative Trait Loci for Panicle Layer Uniformity Identified in Doubled Haploid Lines of Rice in Two Environments

Uniformity of stem height in rice directly affects crop yield potential and appearance, and has become a vital index for rice improvement. In the present study, a doubled haploid (DH) population, derived from a cross between japonica rice Chunjiang 06 and indica rice TN1 was used to analyze the quantitative trait locus (QTL) for three related traits of panicle-layer-uniformity; that is, the tallest panicle height, the lowest panicle height and panicle layer disuniformity in two locations: Hangzhou (HZ) and Hainan (HN). A total of 16 QTLs for three traits distributed on eight chromosomes were detected in two different environments. Two QTLs, qTPH -4 and qTPH -8 were co-located with the QTLs for qLPH -4 and qLPH -8, which were only significant in the HZ environment, whereas the qTPH -6 and qLPH -6 located at the same interval were only significant in the HN environment. Two QTLs, qPLD -10-1 and qPLD -10-2, were closely linked to qTPH-10 , and they might have been at the same locus. One QTL, qPLD -3, was detected in both environments, explaining more than 23% of the phenotypic variations. The CJ06 allele of qPLD -3 could increase the panicle layer disuniformity by 9.23 and 4.74 cm in the HZ and HN environments. Except for qPLD -3, almost all other QTLs for the same trait were detected only in one environment, indicating that these three traits were dramatically affected by environmental factors. The results may be useful for elucidation of the molecular mechanism of panicle-layer-uniformity and marker assisted breeding for super-rice.     

Quantitative Trait Loci for Panicle Layer Uniformity Identified in Doubled Haploid Lines of Rice in Two Environments

Uniformity of stem height in rice directly affects crop yield potential and appearance, and has become a vital index for rice improvement. In the present study, a doubled haploid （DH） population, derived from a cross between japonica rice Chunjiang 06 and indica rice TN1 was used to analyze the quantitative trait locus （QTL） for three related traits of paniclelayer-uniformity; that is, the tallest panicle height, the lowest panicle height and panicle layer disuniforrnity in two locations：Hangzhou （HZ） and Hainan （HN）. A total of 16 QTLs for three traits distributed on eight chromosomes were detected in two different environments. Two QTLs, qTPH-4 and qTPH-8 were co-located with the QTLs for qLPH-4 and qLPH-8, which were only significant in the HZ environment, whereas the qTPH-6 and qLPH-6 located at the same interval were only significant in the HN environment. Two QTLs, qPLD-10.1 and qPLD-10.2, were closely linked to qTPH-10, and they might have been at the same locus. One QTL, qPLD-3, was detected in both environments, explaining more than 23% of the phenotypic variations. The CJ06 allele of qPLD-3 could increase the panicle layer disuniformity by 9.23 and 4.74 cm in the HZ and HN environments. Except for qPLD-3, almost all other QTLs for the same trait were detected only in one environment, indicating that these three traits were dramatically affected by environmental factors. The results may be useful for elucidation of the molecular mechanism of panicle-layer-uniformity and marker assisted breeding for super-rice.     

Quantitative trait loci for glucosinolate accumulation in Brassica rapa leaves

Glucosinolates and their breakdown products have been recognized for their effects on plant defense, human health, flavor and taste of cruciferous vegetables. Despite this importance, little is known about the regulation of the biosynthesis and degradation in Brassica rapa. Here, the identification of quantitative trait loci (QTL) for glucosinolate accumulation in B. rapa leaves in two novel segregating double haploid (DH) populations is reported: DH38, derived from a cross between yellow sarson R500 and pak choi variety HK Naibaicai; and DH30, from a cross between yellow sarson R500 and Kairyou Hakata, a Japanese vegetable turnip variety. An integrated map of 1068 cM with 10 linkage groups, assigned to the international agreed nomenclature, is developed based on the two individual DH maps with the common parent using amplified fragment length polymorphism (AFLP) and single sequence repeat (SSR) markers. Eight different glucosinolate compounds were detected in parents and F(1)s of the DH populations and found to segregate quantitatively in the DH populations. QTL analysis identified 16 loci controlling aliphatic glucosinolate accumulation, three loci controlling total indolic glucosinolate concentration and three loci regulating aromatic glucosinolate concentrations. Both comparative genomic analyses based on Arabidopsis-Brassica rapa synteny and mapping of candidate orthologous genes in B. rapa allowed the selection of genes involved in the glucosinolate biosynthesis pathway that may account for the identified QTL.     

世代重叠群体多个QTL最优化选择

一种扩展的方法能够在一个世代重叠的群体内对多个数量性状位点选择进行最优化,目的是为了在整个计划期内获得最大的累积反应加权和。该模型允许群体有多个性别年龄组、公母畜间有不同的年龄组数、各年龄组有不同的遗传贡献。整个最优化问题被描述成一个多阶段系统优化控制问题,通过一个向前和向后的迭代循环解决。用一个世代重叠的实际育种猪群的参数来评价该方法的选择效果,并和标准QTL选择和常规BLUP选择进行比较。模拟结果表明,优化选择要优于标准QTL选择和常规BLUP选择。群体结构对优化选择的影响比较明显。优化QTL选择和标准QTL选择在世代重叠的群体内比在世代离散的群体内的选择优势更明显,相对于常规BLUP选择,能够获得更大的选择优势。在世代重叠群体内随着2岁公畜遗传贡献的增大,优化选择相对于常规BLUP选择的优势越明显。     

Optimizing Selection on Multiple Identified Quantitative Trait Loci in Population with Overlapping Generations

A method was developed to model and optimize selection on multiple identified quantitative trait loci (QTLs) and polygenic estimated breeding value, in order to maximize a weighted sum of cumulative response to selection over multiple years in a population with overlapping generations. The model allows for a population with multiple sex-age classes, different number of age class between sires and dams, and varied genetic contribution of the age class. The optimization problem was formulated as a multiple-stage optimal control problem and solved by a forward and backward iteration loop. The practical utility of this method was illustrated in an example of pig breeding population with overlapping generations. The selection response of this method was compared with standard QTL selection and conventional best linear unbiased prediction (BLUP) selection. Simulation results show that optimal selection achieved greater selection response than either standard QTL or conventional BLUP selections. The influence of population structure on optimal selection was significant. Optimal QTL selection and standard QTL selection were more favorable in a population with overlapping generations than discrete generations, and obtained more benefits relative to conventional BLUP selection in a population with overlapping generations. Optimal QTL selection relative to conventional BLUP selection is also more favorable following increase of genetic contribution of two-year-old boars and sows in a population with overlapping generations.     

雄性不交换条件下F2群体区间标记——QTL定位的相关方法（英文）

提出了雄性不交换条件下F2群体区间标记定位QTL的相关方法,并且对其适用的条件进行了讨论,通过对分子区间标记进行赋值,计算在无交叉干涉条件下分子标记与表型值的简单相关系数,并在此基础上进行连锁检验,在特定条件下可以估计数量性状座位（QTL）与分子标记座位间的连锁值。     

利用水稻重组自交系群体定位谷粒外观性状的数量性状基因

用区间作图和混合线性模型的复合区间作图两种方法,对水稻（Oryza sativa L）珍汕97和明恢63组合的重组自交系群体的谷粒外观性状－粒长,粒宽和粒形进行了数量性状基因（QTL）定位,用区间作图法在LOD≥2．4水平上（近拟于a=0.005),1998年对粒长,粒宽和粒形分别检测到6,2放2个QTLs,1999年对以上3个性状分别检测到3,2和2个QTLs,其中7个QTLs在两年均检测到,位于第3染色体RG393－C1087区间的QTL效应大,同时影响粒长和粒形,两年贡献分别为57．5％,61．4％和26．7％,29．9％,位于第5染色体RG360－C734B区间的QTL效应大,同时影响粒宽和粒形,两年贡献率分别为44．2％,53．2％和32．1％和36．0％,用混合线性模型的复合区间作图法在P＝0．005水平上,对粒长,粒宽和粒形分别检测到8,5和5个QTLs,共解释各自性状变异的58．81％,44．75％和57．47％,只检测到1个QTL与环境之间存在的显互作。     

Mapping Quantitative Trait Loci for Grain Appearance Traits of Rice Using a Recombinant Inbred Line Population

A linkage map consisting of 221 markers was constructed based on a recombinant inbred line (RIL) population from the cross between Zhenshan 97 and Minghui 63. Quantitative trait loci (QTL) mapping was carried out for grain appearance traits such as grain length, grain width and grain shape in rice in 1998 and 1999. Based on interval mapping method at the threshold LOD≥2.4, six, two and two QTLs were detected for grain length, grain width and grain shape, respectively, in 1998; In 1999, three, two and two QTLs were identified for the three traits, respectively. Of them, seven QTLs were simultaneously identified in both of the years. The QTL with large effects located in the interval RG393-C1087 on chromosome 3 not only controlled the grain length, but also influenced the grain shape. It explained 57.5%, 61.4% and 26.7%, 29.9% of phenotypic variation of the grain length and the grain shape in two years, respectively. The QTL with large effects located in the interval RG360-C734B on chromosome 5 affected the grain width and the grain shape. It explained 44.2%, 53.2% and 32.1%, 36.0% of phenotypic variation of the grain width and the shape in two years, respectively. Eight, five and five QTLs were identified for the grain length, width and shape, respectively, based on mixed linear-model composite interval mapping method at P =0.005. Their general contributions were 58.81%, 44.75%, and 57.47%. One QTL for the grain length was found to be significant interaction with environment.     

Quantitative Trait Loci Mapping of Flag-leaf Ligule Length in Rice and Alignment with ZmLG1 Gene

A doubled haploid （DH） population, which consists of 120 lines derived from anther culture of a typical indica and japonica hybrid‘CJ06＇/‘TNI＇, was used in this study. Ligule lengths of flag leaf were investigated for quantitative trait loci （QTL） mapping using the DH population. Five QTLs （qLL-2, qLL.4, qLL-6, qLL-IO and qLL-12） controlling the ligule length （LL） were detected on chromosomes 2, 4, 6, 10 and 12, with the variances explained 11.4%, 13.6%, 27.8%, 22.1% and 11.0%, respectively. Using four known genes of ZmGL1, ZmGL2, ZmGL3 and ZmGL4 in maize from the MaizeGDB, their homologs in rice were aligned and integrated into the existing simple sequence repeats linkage map by in silico mapping. A ZmLG1 homolog gene, OsLG1 encoding a squamosa promoter binding protein, was located between the markers RM255 and RM280, which is just identical to the interval of qLL.4 on the long arm of chromosome 4. The results are beneficial to dissection of the ligule molecular mechanism and the study of cereal evolution.     

油菜油分、蛋白质和硫苷含量相关性分析及QTL定位

为定位与油分、蛋白质和硫苷含量等品质性状相关的数量性状位点（QTL）,以2个含油量较高的甘蓝型油菜（Brassica napus）品系8908B和R1为研究材料,配置正反交组合。在正反交F2代群体中,含油量和蛋白质含量都存在极显著的负相关,相关系数分别为-0．68和-0．81,含油量和硫苷含量相关性不显著：蛋白质含量和硫苷含量在正交群体中相关性不显著,但在反交群体中存在显著负相关（相关系数r=-0．45）。利用正交F2代群体中的118个单株,构建了包含121个标记的遗传连锁图谱,图谱长1298．7cM,有21个连锁群（LGs）。采用复合区间作图法,在连锁图上定位了2个与含油量有关的QTL,分别位于LG8和LG10,其贡献率分别为4．8％和13．7％,增效基因都来源于R1;定位了2个与蛋白质含量有关的QTL：pr01和pr02,分别位于LG1和LG3,其贡献率分别为15．2％和14．1％,位点pr07由8908B提供增效基因,pro2则由R1提供增效基因：定位了4个与硫苷含量有关的QTL,其中LG20上有2个,LG4和LG8上各1个,它们的贡献率在1．9％-25．4％之间,除LG20上glu7的增效基因来自R1外,其余3个QTL位点均由8908B提供增效基因。     

猪2号染色体遗传连锁图谱的构建与QTL定位分析

构建了猪2号染色体的遗传连锁图谱,并进一步进行了重要生产性状数量性状位点的定位,结果表明,7个微卫星位点均为中高度多态性位点,多态信息含量为0．40182－0．58477,可以满足遗传连锁图谱构建的要求,构建的资源家系遗传连锁图谱总长152．9cM,位点的排列顺序与USDA结果一致,但除了Sw2516与Sw1201标记区间外,所有标记区间距离均大于USDA图谱,将连锁图谱与性状记忆结合起来,进一步进行了猪数量性状位点定位的研究,在2号染色体发现了显著影响活体估测瘦肉率等活体估测性状的QTLs,此外还发现眼肌高度和背最长肌大理石纹的QTLs,其中影响活体估测瘦肉率的QTL达到了染色体显著的水平（P＜0．01）,且解释性状的表型变异达21．55％,影响眼肌高度和背最长肌大理石纹的QTLs分别可以解释10．12％和10．97％的表型变异,影响活体估测性状的QTLs加性效应与显性效应作用方向相反,影响眼肌高度的QTL加性效应与显性效应相同,在大白猪中具有增效等位基因,定位的QTLs效应较大,为在群体中开展分子标记辅助育种奠定了理论基础。     

利用水稻重组自交系群体对一些重要农艺性状进行基因定位和互作分析

对水稻（OryzasativaL．）籼（indica）、粳（Japonica）交（窄叶青8号×京系17）通过一粒传获得了一个自交9代的重组自交系（RIL）群体,该群体含有107个稳定纯合的株系,通过构建分子连锁图谱,对水稻播抽期、株高、每穗颖花数、每穗实粒数、200粒重和结实率进行数量性状基因座位（QTL）分析,定位了影响播抽期的2个QTLs、株高的2个QTLs、每穗颖花数的2个QTLs和每穗实粒数的1个QTL。其中,控制播抽期的1个QTL即qHD－8为主效基因,控制株高的1个QTL即qPH－1为主效基因,其余为微效基因。同时分析了影响水稻生产力的数量性状基因座位间的互作。结果表明,影响播抽期、株高、每穗颖花数、每穗实粒数和结实率的互适型互作共有24个,对性状有6．2％～10．9％的贡献率。     

猪部分内脏器官性状和乳头数的QTL检测

对内脏器官重量性状的QTL定位研究,所见报道不多;对于猪的繁殖性状,尚需做进一步的探讨。本研究在总共214头(180头F2个体)组成的资源家系中,在猪的SSC4、SSC6、SSC7、SSC8 和 SSC13上共选取39个微卫星标记,检测了8种内脏器官的重量性状:心重 (HW)、肺重 (LW)、肝 胆重 (LGW)、脾重 (SPW)、胃重 (STW)、小肠重(SIW)、大肠重(LIW) 和肾重(KW);其他一些胴体性状:胴体长性状1(自第一颈椎,CL1)、胴体长性状2(自第一胸椎,CL2)、肋骨数(RNS)和繁殖性状乳头数(TNS)的QTL定位。结果表明,检测到3个染色体极显著水平的QTL(P≤0.01),它们是HW QTL定位在SSC6上30 cM处,RNS QTL定位在SSC7上115 cM处和TNS QTL定位在SSC7上 110 cM处;另外6个染色体显著水平的QTL(P≤0.05)是:LW(SSC13上119 cM处)、LGW(SSC6上94 cM处)、SPW(SSC8上106 cM处)、SIW(SSC 4上0 cM处)、LIW(SSC 4上170 cM 处)和TNS(SSC 6上95 cM处)。上述QTL解释的表型变异从 0.04% 到 14.06%,有些位点的 QTL 可以解释表型变异的 10%以上,如 HW 的 QTL 解释表型变异的9.52%、SIW的QTL解释表型变异的13.47%、定位在SSC6上的TNS QTL解释表型变异的14.06%,而定位在 SSC7上的TNS QTL解释表型变异的11.30%。多数内脏器官重量性状的QTL定位结果未见报道。胴体长未见显著水平的QTL,而在SSC7上定位染色体极显著水平的肋骨数QTL。     

Quantitative trait loci analysis of phytate and phosphate concentrations in seeds and leaves of Brassica rapa

Phytate, being the major storage form of phosphorus in plants, is considered to be an anti-nutritional substance for human, because of its ability to complex essential micronutrients. In the present study, we describe the genetic analysis of phytate and phosphate concentrations in Brassica rapa using five segregating populations, involving eight parental accessions representing different cultivar groups. A total of 25 quantitative trait loci (QTL) affecting phytate and phosphate concentrations in seeds and leaves were detected, most of them located in linkage groups R01, R03, R06 and R07. Two QTL affecting seed phytate (SPHY), two QTL affecting seed phosphate (SPHO), one QTL affecting leaf phosphate and one major QTL affecting leaf phytate (LPHY) were detected in at least two populations. Co-localization of QTL suggested single or linked loci to be involved in the accumulation of phytate or phosphate in seeds or leaves. Some co-localizing QTL for SPHY and SPHO had parental alleles with effects in the same direction suggesting that they control the total phosphorus concentration. For other QTL, the allelic effect was opposite for phosphate and phytate, suggesting that these QTL are specific for the phytate pathway.     

基于CSSL的高密度物理图谱定位水稻分蘖角度QTL

对以籼稻9311为遗传背景携带粳稻日本晴基因组的染色体片段置换系（CSSL）的遗传图谱进行分子标记加密,构建了含250个多态标记的高密度物理图谱。以119个CSSLs为材料,P≤0.001为阈值,筛选到分蘖角度与受体亲本9311差异极显著的10个系。结合物理图谱和代换作图方法,共鉴定出5个分蘖角度QTL,其中qTA11的加性效应表现为增效作用,来源于9311的等位基因;其余4个QTL的加性效应为减效作用,均来源于日本晴的等位基因。qTA6-1和qTA6-2分别被定位于第6染色体RM253–RM527之间的3.55Mb区段和RM3139–RM494的1.65Mb区间;qTA9被定位于第9染色体RM257–RM189之间的3.40Mb区段;qTA10被定位在第10染色体RM222–S10-1之间的2.10Mb区段;qTA11被定位于第11染色体RM1761–RM4504之间的3.30Mb区间。以上研究结果为水稻分蘖角度QTL的精细定位和株型育种提供了依据。     

利用一个水稻RIL群体定位控制淀粉特性的QTL

利用个山籼粳(Oryza sativa L.)杂交发展成的重组自交系(RIL)群体研究影响淀粉特性的遗传因子,测定了一系列淀粉特性有关性状,包括直链淀粉含量、胶稠度、淀粉糊粘度、胶的质地、糊化温度、热学特性、回生特性等22个参数。共定位了44个QTL,分布在第2～6、8、9、11染色体上,每个性状所定位的QTL在1到4个不等。其中有2个是主基因,一个是第6染色体上的Wx基因,它控制直链淀粉含量、胶稠度、淀粉糊粘度、胶的质地、回生特性等性状,另一个足第6染色体上的alk基因,它控制糊化温度与热学特性等性状,其他QTL都是微效基因,在第9染色体上RZ404和G295区间系首次检测到,它控制淀粉胶的硬度(hardness)、胶粘性(gumminess)、咀嚼性(chewiness)、回生淀粉的最高糊化温度、回生率等性状,这些性状都未曾研究过。     

QTL and QTL x environment effects on agronomic and nitrogen acquisition traits in rice

Agricultural environments deteriorate due to excess nitrogen application.Breeding for low nitrogen responsive genotypes can reduce soil nitrogen input.Rice genotypes respond variably to soil available nitrogen.The present study attempted quantification of genotype x nitrogen level interaction and mapping of quantitative trait loci (QTLs) associated with nitrogen use efficiency (NUE) and other associated agronomic traits.Twelve parameters were observed across a set of 82 double haploid (DH) lines derived from IR64/Azucena.Three nitrogen regimes namely,native (0 kg/ha; no nitrogen applied),optimum (100 kg/ha) and high (200 kg/ha) replicated thrice were the environments.The parents and DH lines were significantly varying for all traits under different nitrogen regimes.All traits except plant height recorded significant genotype x environment interaction.Individual plant yield was positively correlated with nitrogen use efficiency and nitrogen uptake.Sixteen QTLs were detected by composite interval mapping.Eleven QTLs showed significant QTL x environment interactions.On chromosome 3,seven QTLs were detected associated with nitrogen use,plant yield and associated traits.A QTL region between markers RZ678,RZ574 and RZ284 was associated with nitrogen use and yield.This chromosomal region was enriched with expressed gene sequences of known key nitrogen assimilation genes.     

Identification of Quantitative Trait Loci for Rice Quality in a Population of Chromosome Segment Substitution Lines

The demand for high quality rice represents a major issue in rice production. The primary components of rice grain quality include appearance, eating, cooking, physico-chemical, milling and nutritional qualities. Most of these traits are complex and controlled by quantitative trait loci (QTLs), so the genetic characterization of these traits is more difficult than that of traits controlled by a single gene. The detection and genetic identification of QTLs can provide insights into the genetic mechanisms underlying quality traits. Chromosome segment substitution lines (CSSLs) are effective tools used in mapping QTLs. In this study, we constructed 154 CSSLs from backcross progeny (BC3F2) derived from a cross between 'Koshihikari' (an Oryza sativa L. Ssp. Japonica variety) as the recurrent parent and 'Nona Bokra' (an O. Sativa L. Ssp. Indica variety) as the donor parent. In this process, we carried out marker-assisted selection by using 102 cleaved amplified polymorphic sequence and simple sequence repeat markers covering most of the rice genome. Finally, this set of CSSLs was used to identify QTLs for rice quality traits. Ten QTLs for rice appearance quality traits were detected and eight QTLs concerned physico-chemical traits. These results supply the foundation for further genetic studies and breeding for the improvement of grain quality.     

利用一个水稻RIL群体定位控制淀粉特性的QTL

利用一个由籼粳(Oryza sativa L.)杂交发展成的重组自交系(RIL)群体研究影响淀粉特性的遗传因子,测定了一系列淀粉特性有关性状,包括直链淀粉含量、胶稠度、淀粉糊粘度、胶的质地、糊化温度、热学特性、回生特性等22个参数.共定位了44个QTL,分布在第2～6、8、9、11染色体上,每个性状所定位的QTL在1到4个不等.其中有2个是主基因,一个是第6染色体上的Wx基因,它控制直链淀粉含量、胶稠度、淀粉糊粘度、胶的质地、回生特性等性状,另一个是第6染色体上的alk基因,它控制糊化温度与热学特性等性状,其他QTL都是微效基因,在第9染色体上RZ404和G295区间系首次检测到,它控制淀粉胶的硬度(hardness)、胶粘性(gumminess)、咀嚼性(chewiness)、回生淀粉的最高糊化温度、回生率等性状,这些性状都未曾研究过.     

Identification of Quantitative Trait Loci for Grain Appearance and Milling Quality Using a Doubled-Haploid Rice Population

Improving grain quality, which is composed primarily of the appearance of the grain and its cooking and milling attributes, is a major objective of many rice-producing areas in China. In the present study, we conducted a marker-based genetic analysis of the appearance and milling quality of rice （Oryza sativa L.） grains using a doubled-haploid population derived from a cross between the indica inbred Zhenshan 97 strain and the japonica inbred Wuyujing 2 strain. Quantitative trait locus （QTL） analysis using a mixed linear model approach revealed that the traits investigated were affected by one to seven QTLs that individually explained 4.0%-30.7% of the phenotypic variation. Cumulatively, the QTL for each trait explained from 12.9% to 61.4% of the phenotypic variation. Some QTLs tended to have a pleiotropic or location-linked association as a cause of the observed phenotypic correlations between different traits. Improvement of the characteristics of grain appearance and grain weight, as well as an improvement in the milling quality of rice grains, would be expected by a recombination of different QTLs using marker-assisted selection.