Conditional and unconditional mapping of quantitative trait loci underlying plant height and tiller number in rice (Oryza sativa L.)grown at two nitrogen levels

In this study, we used 127 double haploid (DH) lines to analyze agricultural traits of rice. The DH lines, derived from a ZYQ8 (indica)/JX17 (japonica) cross by anther culture, contained 160 RFLP and 83 SSR markers. Unconditional and conditional quantitative trait loci (QTL) mapping was conducted to analyze plant height (PH) and tillers per plant (TP) at ?ve growth stages that were grown at two nitrogen levels. Fourteen PH and 13 TP unconditional QTL were identified in the di?erent growth stages, including 19 QTL from high-nitrogen (HN) and 14 QTL from low-nitrogen (LN) conditions. The conditional QTL for 14 genomic regions under LN/HN conditions showed that there was a significant effect on PH and TP across the different stages. Only one conditional QTL, ph2-3, was unable to be detected in unconditional mapping. More QTL were detected in the ?rst four rice growth stages than in the final stage. Furthermore, a line from the DH mapping population, DH78, was identified in extreme phenotypes of PH and TP that exhibited dwarfism and less-tiller (dft) characters. The gene dft1 was mapped to chromosome 2 using a backcrossed population of DH78/JX17 through a mapbased cloning strategy. The location of dft1 coincided with the mapping region of the small-LOD peak, QTL ph2 and tp2, which were identified in plants grown in low-nitrogen conditions. Further backcrossing and fine-mapping successfully delimited the dft1 locus to a 91 kb region.     

控制水稻剑叶形态相关性状的数量基因位点(QTL)的定位

水稻籽粒中一半以上的碳水化合物来自剑叶的光合作用,剑叶形态改良一直是水稻株型育种的一个重要目标．利用一个日本主要种植的粳稻品种越光（轮回亲本）和一个印度的籼稻品种Kasalath杂交产生的回交重组自交系群体（backcross recombinant inbred lines,BILs）对剑叶形态中的3个主要性状（剑叶长、叶宽以及其叶面积）进行了相关分析及其数量基因位点（quantitative trait loci,QTL）的定位．研究表明,控制剑叶形态的3个主要性状间存在极显著的正相关,并检测到影响3个性状的8个QTL,分布在第1,3,4,6条染色体上,贡献率介于4．94％～22．07％,其中第4染色体上C1016标记和第6染色体上C556标记附近的共有6个QTL,其两侧的紧密分子标记在水稻株型分子育种上具有一定应用价值．     

水稻芒长及其分布特征相关QTL的定位

水稻芒的性状与驯化过程密切相关,具体表现为芒长短和芒的分布等．利用一个无芒品种越光（轮回亲本）和一个有芒品种Kasalath杂交产生的回交重组自交系群体,在上海、海南两地对芒长和芒的分布（芒出现比例）进行了相关分析及其相关基因（QTL）定位,结果发现这两个性状间存在显著的正相关．共检测到影响这两个性状的12个QTL,分布在6条染色体上的7个区域,贡献率介于2．90％-53．24％,其正效应大多来自有芒亲本Kasalath,但也有3个QTL正效应来自无芒亲本越光,并对这个现象产生的原因进行了讨论．本研究检测到的QTL及其两侧的分子标记可以用于水稻驯化的研究和理想型无芒品种分子辅助育种．     

Identification of salt-tolerance QTL in rice (Oryza sativa L.)

Quantitative trait loci (QTLs) controlling salt-tolerance at the seedling stage in rice (Oryza sativa L.) were identified by interval mapping (SIM) and composite interval mapping (CIM) using a doubled haploid population ZJDH and its high resolution genetic linkage map. The population was derived from an inter-subspecific cross between an indica variety Zhaiyeqing8 (ZYQ8) and a japonica variety Jingxi17 (JX17). Analysis of survival days of seedlings treated with 0.7% NaCI revealed that a major salt-tolerance quantitative trait locus (QTL), Std, was present between markers RG612 and C131 on chromosome 1 when using both MAPMAKER/QTL 1.1 and PLABQTL 1.0 (SIM). Its allele which contributes to salt-tolerance was from ZYQ8. In addition, seven more QTLs which give additive effect on salt-tolerance are identified when using PLABQTL (CIM), and most of them were from JX17.     

Genetic analysis and mapping of rice （Oryza sativa L.） male-sterile （OsMS-L） mutant

A rice male-sterile mutant OsMS-L of japonica cultivar 9522 background, was obtained in M4 population treated with ^60Co γ-Ray. Genetic analysis indicated that the male.sterile phenotype was controlled by a single recessive gene. Results of tissue section showed that at microspore stage, OsMS-L tapetum was retarded. Then tapetal calls expanded and microspores degenerated. No matured pollens were observed in OsMS-L anther locus. To map OsMS-L locus, an F2 population was constructed from the cross between the OsMS-L (japonica) and LongTeFu B(indica). Firstly, the OsMS-L locus was roughly mapped between two SSR markers, RM109 and RM7562 on chromosome 2. And then eleven polymorphic markers were developed for further fine fine-mapping. At last the OsMS-L locus was mapped between the two lnDel markers, Lhsl0 and Lhs6 with genetic distance of 0.4 cM, respectively. The region was delimited to 133 kb. All these results were useful for further cloning and functional analysis of OsMS-L.     

Characterization and mapping of a lesion mimic mutant in rice （Oryza sativa L.）

A rice initiation-type lesion mimic mutant (lmi) was identified, which was isolated from an indica rice Zhongxian 3037 through γ radiation mutagenesis. Trypan blue staining and sterile culture revealed that the mutant spontaneously developed lesions on the leaves in a developmentally regulated and light-dependent manner. Genetic analysis indicated that the lesion mimic trait was controlled by a single resessive locus. Using public molecular markers and an F2 population derived from lmi and 93-11, we mapped the lmi locus to the short arm of chromosome 8, nearby the centromere, between two SSR markers RM547 and RM331. The genetic distance was 1.2 and 3.2 cM, respectively. Then according to the public rice genomic sequence between the two SSR markers, lmi was further finely tagged by three CAPS markers: C4135-8, C4135-9 and C4135-10. And lmi locus was a co-segregated with marker C4135-10, providing a starting point for lmi gene cloning.     

Fine mapping of an incomplete recessive gene for leaf rolling in rice （Oryza sativa L.）

Genetic analysis and fine mapping of genes controlling leaf rolling were conducted using two backcrossed generations （BC4F2, BC4F3） derived from a cross between QMX, a non-rolled leaf cultivar as a recurrent parent, and JZB, a rolled leaf NIL of ZB as a donor parent. Results indicated that leaf rolling was mainly controlled by an incompletely recessive major gene, namely rl（t）, and at the same time, affected by quantitative trait loci （QTLs） and/or the environment. A genetic linkage map was constructed using MAPMAKER/EXP3.0 with eight polymorphic markers on chromosome 2, which were screened by BAS method from 500 SSR markers and 15 newly developed insertion/deletion （InDel） markers. The position of rl（t） was estimated with composite interval mapping （CIM） method using WinQTLcart2.5. Gene rl（t） was mapped between markers InDel 112 and RM3763, and 1.0 cM away from InDel 112 using 241 plants in BC4F2 population. To fine map r（t）, one BC4F3 line with 855 plants was generated from one semi-rolled leaf plant in BC4F2. Four new polymorphic InDel markers were developed, including InDel 112.6 and InDel 113 located between markers InDe1112 and RM3763. Based on the information of recombination offered by 191 rolled leaf plants and 185 non-rolled leaf plants from the BC4F3 line ,we mapped r（t） to a 137-kb region between markers InDel 112.6 and InDel 113. Homologous gene analysis suggested that r（t）was probably related to the process of leaf development regulated by microRNA.     

QTL analysis of flag leaf in barley （Hordeum vulgate L.） for morphological traits and chlorophyll content

To understand genetic patterns of the morphological and physiological traits in flag leaf of barley, a double haploid （DH） population derived from the parents Yerong and Franklin was used to determine quantitative trait loci （QTL） controlling length, width, length/width, and chlorophyll content of flag leaves. A total of 9 QTLs showing significantly additive effect were detected in 8 intervals on 5 chromosomes. The variation of individual QTL ranged from 1.9% to 20.2%. For chlorophyll content expressed as SPAD value, 4 QTLs were identified on chromosomes 2H, 3H and 6H; for leaf length and width, 2 QTLs located on chromosomes 5H and 7H, and 2 QTLs located on chromosome 5H were detected; and for length/width, I QTL was detected on chromosome 7H. The identification of these QTLs associated with the properties of flag leaf is useful for barley improvement in breeding programs.     

Characterization and fine mapping of an early senescence mutant （es-t） in Oryza sativa L.

An es-t (early senescence-temporary) mutant, produced by ethylene methylsulfonate treatment of strain Nipponbare, was identified in rice. The leaves of es-t appeared yellow at the seedling stage, and had decreased chlorophyll content. Rust spots were found during growth in es-t, especially at the leaf margin and tip. The plants showed a typical early-senescence phenotype at the milky stage. The leaf surface of es-t appeared smoother than wild-type leaves under a scanning electron microscope, because the lea...     

Genetic analysis and gene mapping of leafy head （lhd）, a mutant blocking the differen-tiation of rachis branches in rice （Oryza sativa L.）

Flowers, fruits and seeds are products of plant re- productive development and provide the important sources of foods for humans. Therefore, the moleculargenetic mechanisms of floral development have been ahotspot of research of plant developmental biology[1]. Rice is one of the most important staple food crops. Theoutcome of its reproductive development would determine the yield and quality of grains. Rice is also a model plantof cereals. Hence, the study of rice reproductivedevelopment, esp…     

Morphological and physiological analysis of narrow and striped leaf 1 （nsl1） mutant of rice （Oryza sativa L.） and the gene mapping

The shape and color of rice leaves are impor- tant agronomic traits that directly influence the proportion of sunlight energy utilization and ultimately affect the yield and quality. A new mutant exhibiting stable inheritance was identified as derived from ethyl methane sulfonate （EMS）-treated restorer Jinhui 10, tentatively named as narrow and striped leaf 1 （nsll）. The nsll displayed pale white leaves at the seeding stage and then white striped leaves in parallel to the main vein at the jointing stage. Meanwhile, its leaf blades are significantly narrower than the control group of Jinhui 10. The chloroplast structures of cells in the white striped area of the nsll mutant break down, and the photosynthetic pigments are significantly lower than that of the wild type. Moreover, fluorescence parameters, such as Fo, Fv/Fm, ФpsⅡ, qP, and ETR, in the nsll mutant are significantly lower than those of the wild type, and the photosynthetic efficiency is also significantly decreased. These changes in leaf color and shape, together with physiological changes in the nsll, result in smaller plant height and a decrease in the most important agro- nomic traits, such as the number of grains per panicle, grain weight, etc. Genetic analysis shows that the narrow and striped traits of the nsll mutant are controlled by a single recessive nuclear gene, which is located between InDel 16 and InDel 12 in chromosome 3. The physical distance is 204 kb. So far, no similar genes of such leaf color and shape in this area have been reported, This study has laid asolid foundation for the gene cloning and function analysis of NSL 1.     

Fine mapping of <Emphasis Type="Italic">qHUS6.1</Emphasis>, a quantitative trait locus for silicon content in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Silicon is essential for optimal growth of rice (Oryza sativa L.). This study was conducted to fine map qHUS6.1, a quantitative trait locus (QTL) for rice hull silicon content previously located in the interval RM510–RM19417 on the short arm of chromosome 6, and to analyze the effect of this QTL on the silicon content in different organs of rice. Selfed progenies of a residual heterozygous line of rice were detected using 13 microsatellite markers in the vicinity of qHUS6.1. Three plants with overlapping heterozygous segments were selected. Three sets of near isogenic lines (NILs) were developed from the selfed progenies of the 3 plants. They were grown in a paddy field and the silicon contents of the hull, flag leaf, and stem were measured at maturity. Based on analyses of the phenotypic distribution and variance among different genotypic groups in the same NIL set, a significant genotypic effect was shown in the NIL set that was heterogenous in the interval RM19410–RM5815, whereas a significant effect was not found in the remaining 2 NIL sets that were heterogenous in either of the intervals RM4923–RM19410 or RM19417–RM204. On comparison among the physical positions of the 3 heterogenous segments, qHUS6.1 was delimited to a 64.2-kb region flanked by RM19410 and RM19417 that contains nine annotated genes according to the genome sequence of Nipponbare. This QTL showed strong effects on all of the three traits tested, and the enhancing alleles were always derived from the paternal line Milyang 46. The present study will facilitate the cloning of qHUS6.1 and the exploration of new genetic resources for QTL fine mapping.     

Genetic diversity of rice cultivars （Oryza sativa L.） in China and the temporal trends in recent fifty years

Public concern is often expressed at cultivars because the domestication and modern plant breeding have led to a reduction in the genetic diversity of crops and loss of genes, which could result in crops' genetic vulnerability to changes in the spectrum of pestssity of varieties in this zone is very important to the whole rice production in China. REZV, a important japonica rice production areas with more than 278 thousands ha rice which was about 71% of rice area in north China, accounted fo…     

Genetic analysis and molecular mapping of a presenescing leaf gene psll in rice （Oryza sativa L.）

A rice psl1 （presenescing leaf） mutant was obtained from a japonica variety Zhonghua 11 via radiation of ^60Co-γ in M2 generation. Every leaf of the mutant began to wither after it reached the biggest length, while the leaves of the wild variety could keep green for 25--35 d. In this study, genetic analysis and gene mapping were carried out for the mutant identified. The SSR marker analysis showed that the mutant was controlled by a single recessive gene （psl1） located on chromosome 2. Fine mapping of the psl1 locus was conducted with 34 new STS markers developed around psl1 anchored region based on the sequence diversity between Nipponbare and 93-11. The psl1 was further mapped between two STS markers, STS2-19 and STS2-26, with genetic distances of 0.43 and 0.11 cM, respectively, while cosegregated with STS2-25. A BAC contig was found to span the psl1 locus, the region being delimited to 48 kb. This result was very useful for cloning of the psl1 gene.     

Genetic analysis and molecular mapping of a presenescing leaf gene psl1 in rice (Oryza sativa L.)

A rice psl1 (presenescing leaf) mutant was obtained from a japonica variety Zhonghua 11 via radiation of 60Co-γ in M2 generation. Every leaf of the mutant began to wither after it reached the big-gest length,while the leaves of the wild variety could keep green for 25―35 d. In this study,genetic analysis and gene mapping were carried out for the mutant identified. The SSR marker analysis showed that the mutant was controlled by a single recessive gene (psl1) located on chromosome 2. Fine mapping of the psl1 locus was conducted with 34 new STS markers developed around psl1 anchored region based on the sequence diversity between Nippon-bare and 93-11. The psl1 was further mapped be-tween two STS markers,STS2-19 and STS2-26,with genetic distances of 0.43 and 0.11 cM,respectively,while cosegregated with STS2-25. A BAC contig was found to span the psl1 locus,the region being delim-ited to 48 kb. This result was very useful for cloning of the psl1 gene.     

水稻S_5区候选克隆R2I19的筛选及序列信息学分析

以水稻广亲和品种Cpslo17为材料 ,构建了一个覆盖 9倍核基因组的cosmid文库 ,其平均插入片段约4 0kb。以与广亲和位点紧密联锁的单拷贝分子标记BAC2 3D12的R末端为探针 ,从cosmid文库中筛选得到一个阳性克隆R2I19(～ 32kb)。结合S5位点的高密度连锁图和物理图谱 ,初步确定为S5区候选克隆。对该克隆的 2个TAC亚克隆TRW15 10 (～ 15kb)及TRW15 17(～ 15kb)进行了初步的生物信息学分析 ,证实与已知的水稻基因组序列有很高的同源性 ,并显示其中可能含有与水稻育性相关的基因。     

Identification and mapping of quantitative trait loci controlling cold-tolerance of Chinese common with rice （O.rufipogon Griff.） at booting to flowering stages

An advanced backcross population of rice was used to identify the quantitative trait locus(QTL) controlling the cold-tolerance at booting to flowering stages.The recipient,Guichao 2(GC2),was a commercial Indica rice;the donor Dongxiang common wild rice,was an accession of common wild rice(DXCWR,Oryza rufipogon Griff.).Three QTLs for cold-tolerance were detected on chromosomes 1,6 and 11.Two of them coming from DXCWR could enhance the cold-tolerance of the backcross progenies.Moreover,one sterility QTL that could reduce the seed set rate of the backcross progenies by 78% was mapped on chromosome5.     

Identification and mapping of quantitative trait loci controlling cold-tolerance of Chinese common wild rice (O. rufipogon Griff.) at booting to flowering stages

Cold injury is an important limitation of rice production. Therefore, screening for cold-tolerant genetic resources and the development of highly cold-tolerant cultivars is crucial for higher yield potential and stable yield of rice. There have been several reports on the genetic analysis and QTL mapping of the cold-tolerance at the booting stage. Toriyama et al.[1,2] and Futsuhara et al.[3,4] reported that 4 or more genes were involved in the cold-tolerance. Several QTLs at the booting sta…