Identification of QTLs for Yield and Associated Traits in F₂ Population of Rice

Identification of quantitative trait loci (QTLs) controlling yield and yield-related traits in rice was performed in the F₂ mapping population derived from parental rice genotypes DHMAS and K343. A total of 30 QTLs governing nine different traits were identified using the composite interval mapping (CIM) method. Four QTLs were mapped for number of tillers per plant on chromosomes 1 (2 QTLs), 2 and 3; three QTLs for panicle number per plant on chromosomes 1 (2 QTLs) and 3; four QTLs for plant height on chromosomes 2, 4, 5 and 6; one QTL for spikelet density on chromosome 5; four QTLs for spikelet fertility percentage (SFP) on chromosomes 2, 3 and 5 (2 QTLs); two QTLs for grain length on chromosomes 1 and 8; three QTLs for grain width on chromosomes1, 3 and 8; three QTLs for 1000-grain weight (TGW) on chromosomes 1, 4 and 8 and six QTLs for yield per plant (YPP) on chromosomes 2 (3 QTLs), 4, 6 and 8. Most of the QTLs were detected on chromosome 2, so further studies on chromosome 2 could help unlock some new chapters of QTL for this cross of rice variety. Identified QTLs elucidating high phenotypic variance can be used for marker-assisted selection (MAS) breeding. Further, the exploitation of information regarding molecular markers tightly linked to QTLs governing these traits will facilitate future crop improvement strategies in rice.     

水稻粒长基因GL3的遗传分析和分子标记定位

为了解析水稻粒长的遗传机制,以大粒水稻品种‘80018-TR161-2-1’和小粒水稻品种‘日本小黑稻’及其F2代200个株系和F2：3家系为材料,分析水稻粒长的遗传学性状。结果表明,谷粒长度的分离比在F2及F2：3家系中都表现为3：1,长粒性状受1对隐性核基因控制,命名为GL3。用简单重复序列（simple sequence repeat,ssR）分子标记结合群体分组混合分析的方法,将此种基因定位在水稻第3号染色体上SSR标记PSM379和RM16之间,它们的遗传距离分别为4．0cM和11．2cM。     

Molecular mapping of two semidwarf genes in an indica rice variety Aitaiyin3 (Oryza sativa L.)

Genetic analysis established that Aitaiyin3,a dwarf rice variety derived from a semidwarf cultivar Taiyin1,carries two recessive semidwarf genes.By using simple sequence repeat(SSR)markers,we mapped the two semidwarf genes,sd-1 and sd-t2 on chromosomes 1 and 4,respectively.Sd-t2 was thus named because the semidrawf gene sd-t has already been identified from Aitaiyin 2 whose origin could be traced back to Taivin1.The result of the molecular mappingof sd-1 gene revealed it is linked to four SSR markers found on chromosome 1.These markers are:RM297,RM302,RM212,and OSR3 spaced at 4.7 cM,0 cM,0.8cM and 0 cM,respectively.Sd-t2 was found to be located on chromosome 4 using five SSR markers:two markers,SSR332 and RM1305 located proximal to sd-t2 are spaced 11.6 cM,3.8 cM,respectively,while the three distally located primers,RM5633,RM307,and RM401 are separated by distances of 0.4 cM,0.0 cM,and 0.4 cM,respectively.     

籼稻稻米碾磨与外观品质性状的QTL定位

文章利用籼籼交组合特青/IRBB衍生的重组自交系群体, 在2个环境下对稻米碾磨品质和外观品质进行QTL定位。共计检测到控制稻米碾磨品质的QTL 12个和控制外观品质的QTL 18个, 包括糙米率8个、精米率2个、整精米率2个、粒长7个、粒宽5个和长宽比6个, 这些QTL分布于除第4和12染色体外的其他10条染色体上。其中, 第3染色体涵盖粒形基因GS3的区域对粒长、长宽比、糙米率和整精米率具有较大效应, 其献率分别为56.71%、42.23%、10.05%和4.91%; 第5染色体涵盖粒宽基因GW5的区域对粒宽、长宽比、糙米率和精米率具有较大效应, 表型变异贡献率分别为59.51%、36.68%、19.51%和4.56%。此外, 第6染色体涵盖直链淀粉含量基因Wx的区域对糙米率和精米率具有较小效应。GS3和GW5对糙米率和粒形具有重要作用。     

基于CSSL的水稻抽穗期QTL定位及遗传分析

抽穗期是水稻（Oryza sativa）品种的重要农艺性状之一,适宜的抽穗期是获得理想产量的前提。鉴定和定位水稻抽穗期基因/QTL,分析其遗传效应对改良水稻抽穗期至关重要。以籼稻品种9311（Oryzasativa ssp.indica‘Yangdao 6’）为受体,粳稻品种日本晴（Oryza sativa ssp.japonica‘Nipponbare’）为供体构建的94个染色体片段置换系群体为材料,以P≤0.01为阈值,对置换片段上的抽穗期QTL进行了鉴定。采用代换作图法共定位了4个控制水稻抽穗期的QTL,分别位于第3、第4、第5和第8染色体;QTL的加性效应值变化范围为–6.4––2.7,加性效应百分率变化范围为–6.4%––2.7%;qHD-3和qHD-8加性效应值较大,表现主效基因特征。为了进一步定位qHD-3和qHD-8,在目标区域加密16对SSR引物,qHD-3和qHD-8分别被界定在第3染色体RM3166–RM16206之间及第8染色体RM4085–RM8271之间,其遗传距离分别为13.9cM和6.4cM。研究结果为利用分子标记辅助选择改良水稻抽穗期奠定了基础。     

萍乡显性核不育水稻育性相关基因的定位和遗传分析

萍乡显性核不育水稻(Pingxiang Dominant Genic Male Sterile Rice,PDGMSR)是在水稻中首次发现的显性核不育材料,其育性由两对显性基因互作控制,一对是萍乡显性核不育基因Ms-p,另一对是显性上位恢复基因(dominant epistatic fertility restorer gene,Rfe)。两者共同存在时显性上位恢复基因能抑制不育基因的表达,从而使育性表现可育。本实验用一个对萍乡显性核不育水稻有恢复能力的水稻品种E823与萍乡显性核不育水稻配制杂交组合,将(萍乡核不育水稻/E823)F2作为定位群体,根据F3株系的育性分离,选择育性分离株系对应F2单株(基因型为Ms-pMs-pRefrfe和Ms-pms-pRferfe)构建可育池,用对应F2株系中的不育单株(基因型为Ms-pMs-prferfe或Ms-pms-prferfe)构建不育池,将显性上位恢复基因Rfe定位在水稻10染色体RM311和RM3152一侧,遗传距离分别为7.9cM和3.6cM。根据已有的Ms-p的定位结果,合成10染色体部分微卫星引物,对不育单株进行分析,发现RM171和RM6745位于Ms-p的两侧,距离分别为0.3cM和3.0cM。根据10染色体的测序结果,将Ms-p界定在约730kb的范围内,并构建了Ms-p的电子重叠群。植物显性核不育的育性恢复机理存在“复等位基因”和“显性上位互作”两种假说,贺浩华等用经典的遗传学方法证明了萍乡显性核不育水稻育性恢复的遗传机理属于“显性上位互作”。理论上认为,确定其遗传机理最为有效的方法是基因定位,如果不育基因和恢复基因位于同一位点,则其遗传机理属于“复等位基因”,否则为“显性上位互作”。本实验将不育基因和恢复基因定位在水稻10染色体不同的位点,用基因定位的方法证实了萍乡显性核不育水稻育性恢复的遗传机理属于“显性上位互作”。     

利用染色体片段置换系定位水稻落粒性主效QTL

水稻落粒性是与其生产密切相关的重要性状之一。以7个染色体片段置换系为材料,采用重叠群代换作图法对控制落粒性的2个主效QTL进行定位。结果表明,104个SSR标记在亲本间具有多态性,多态率为68.0%;4个置换系的落粒性与亲本日本晴的落粒性相似,表现难落粒。3个置换系与亲本93-11的落粒性相似,表现易落粒;7个染色体片段置换系在第1和第6染色体上检出7个置换片段,其长度分别为23.6、16.5、6.6、9.9、10.4、20.2和7.1 cM;qSH-1-1被定位在第1染色体RM472-RM1387之间,遗传距离约为6.6 cM。qSH-6-1为新发现的落粒性主效QTL,被定位在第6染色体RM6782-RM3430之间,遗传距离约为4.2 cM。利用染色体片段置换系能准确地定位水稻落粒性QTL,qSH-1-1与qSH-6-1的鉴定和初步定位为其进一步的精细定位、图位克隆及分子标记辅助选择奠定了基础。     

Molecular mapping of two semidwarf genes in an indica rice variety Aitaiyin3 (Oryza sativa L.)

Genetic analysis established that Aitaiyin3, a dwarf rice variety derived from a semidwarf cultivar Taiyin1, carries two recessive semidwarf genes. By using simple sequence repeat (SSR) markers, we mapped the two semidwarf genes, sd-1 and sd-t2 on chromosomes 1 and 4, respectively. Sd-t2 was thus named because the semidrawf gene sd-t has already been identified from Aitaiyin 2 whose origin could be traced back to Taiyin1. The result of the molecular mapping of sd-1 gene revealed it is linked to four SSR markers found on chromosome 1. These markers are: RM297, RM302, RM212, and OSR3 spaced at 4.7 cM, 0 cM, 0.8cM and 0 cM, respectively. Sd-t2 was found to be located on chromosome 4 using five SSR markers: two markers, SSR332 and RM1305 located proximal to sd-t2 are spaced 11.6 cM, 3.8 cM, respectively, while the three distally located primers, RM5633, RM307, and RM401 are separated by distances of 0.4 cM, 0.0 cM, and 0.4 cM, respectively. __________ Translated from Acta Genetica Sinica, 2005, 32 (2) [译自: 遗传学报, 2005,32(2)]     

Map-based cloning proves qGC-6, a major QTL for gel consistency of japonica/indica cross, responds by Waxy in rice (Oryza sativa L.)

In this study, one major QTL affecting gel consistency (GC) of japonica/indica cross was identified on chromosome 6 using a DH population. To understand the molecular mechanism that regulates GC in rice grains, the major QTL (qGC-6) was isolated through a map-based cloning approach utilizing chromosome segment substitution lines (CSSLs). Using 64 plants with extremely soft GC that were selected on recombinant break points between two SSR markers, RM540 and RM8200 in a BC4F2 population, qGC-6 was mapped to a 60-kb DNA region between two STS markers, S26 and S27. These two markers were then used to further identify recombination break points. Finally, qGC-6 was delimited in an interval of a 11-kb region. Gene prediction analysis of the 11-kb DNA sequence containing qGC-6 identified only one putative ORF, which encodes granule-bound starch synthesis protein (Wx protein). Results of sequencing analysis and complementation experiment confirmed that this candidate ORF is responsible for rice GC. Genetic evidences revealed that Wx might contribute equally to the grain amylose content-controlling gene as well as gel consistency. This new information is important to breed rice varieties with improved grain quality.     

Genetic Analysis and Molecular Mapping of a Rolling Leaf Mutation Gene in Rice

A rice mutant with rolling leaf, namely γ-rl, was obtained from M2 progenies of a native indica rice stable strain Qinghuazhan （QHZ） from mutagenesis of dry seeds by γ-rays. Genetic analysis using the F2 population from a cross between this mutant and QHZ indicated the mutation was controlled by a single recessive gene. In order to map the locus for this mutation, another F2 population with 601 rolling leaf plants was constructed from a cross between y-rl and a japonica cultivar 02428. After primary mapping with SSR （simple sequence repeats） markers, the mutated locus was located at the short arm of chromosome 3, flanked by RM6829 and RM3126. A number of SSR, InDel （insertion/deletion） and SNP （single nucleotide polymorphism） markers within this region were further developed for fine mapping. Finally, two markers, SNP121679 and InDe1422395, were identified to be flanked to this locus with genetic distances of 0.08 cM and 0.17 cM respectively, and two SNP markers, SNP75346 and SNPl10263, were found to be co-segregated with this locus. These results suggested that this locus was distinguished from all loci for the rolling leaf mutation in rice reported so far, and thus renamed rl10（t）. By searching the rice genome database with closely linked markers using BLAST programs, an e-physical map covering rl10（t） locus spanning about a 50 kb region was constructed. Expression analysis of the genes predicted in this region showed that a gene encoding putative flavin-containing monooxygenase （FMO） was silenced in γ-rl, thus this is the most likely candidate responsible for the rolling leaf mutation.     

基于CSSL的水稻抽穗期QTL定位及遗传分析

抽穗期是水稻(Oryza sativa)品种的重要农艺性状之一, 适宜的抽穗期是获得理想产量的前提。鉴定和定位水稻抽穗期基因/QTL, 分析其遗传效应对改良水稻抽穗期至关重要。以籼稻品种9311(Oryza sativa ssp. indica ‘Yangdao 6’)为受体,粳稻品种日本晴(Oryza sativa ssp. japonica ‘Nipponbare’)为供体构建的94个染色体片段置换系群体为材料, 以P≤0.01为阈值, 对置换片段上的抽穗期QTL进行了鉴定。采用代换作图法共定位了4个控制水稻抽穗期的QTL, 分别位于第3、第4、第5和第8染色体; QTL的加性效应值变化范围为–6.4 – –2.7, 加性效应百分率变化范围为–6.4%– –2.7%; qHD-3和qHD-8加性效应值较大, 表现主效基因特征。为了进一步定位qHD-3和qHD-8, 在目标区域加密16对SSR引物, qHD-3和qHD-8分别被界定在第3染色体RM3166–RM16206之间及第8染色体RM4085-RM8271之间, 其遗传距离分别为13.9 cM和6.4 cM。研究结果为利用分子标记辅助选择改良水稻抽穗期奠定了基础。     

一个新的水稻叶形突变体(tll1)的遗传分析与精细定位

利用甲基磺酸乙酯(ethylmethane sulphonate, EMS)诱变粳稻品种日本晴获得了一个遗传稳定的叶形突变体 thread-like leaf 1 (tll1)。该突变体在杭州表现为矮化、窄叶, 极端时仅剩主脉, 呈细丝状。将该突变体分别与籼稻品种南京6号、浙辐802和9311进行正反交配组, 遗传分析表明该突变体性状由1对隐性单基因控制。通过SSR和STS分子标记对F₂代分离群体进行遗传定位, 将该基因初步定位在第12染色体SSR标记RM247和RM101之间。随后利用已公布的粳稻品种日本晴和籼稻品种9311的基因组序列, 发展了7对有多态的STS标记, 最终将该基因定位在FL13和FL14之间约94.3 kb的区间内, 为进一步克隆TLL1基因奠定了基础。     

Molecular mapping of two reverse photoperiod-sensitive genic male sterility genes (rpms1 and rpms2) in rice (Oryza sativa L.)

The reverse photoperiod-sensitive genic male sterility (PGMS) and thermo-sensitive genic male sterility (TGMS) lines have an opposite phenotype compared with normal PGMS and TGMS lines widely used by the two-line system in current hybrid rice seed production. Thus, the application of reverse PGMS and TGMS lines can compensate PGMS and TGMS lines in hybrid rice production. YiD1S is a reverse PGMS line, in which pollen fertility is mainly regulated by day-length, but also influenced by temperature. Genetic analysis indicated that male sterility of YiD1S was controlled by two recessive major genes. An F₂ population from a cross between YiD1S and 8528 was developed and used for molecular mapping of the two reverse PGMS genes which were first named rpms1 and rpms2. Both simple sequence repeat (SSR) markers and bulked segregant analysis (BSA) were used in this study. As a result, one reverse PGMS gene (rpms1) was mapped to the interval between SSR markers RM22980 (0.9 cM) and RM23017 (1.8 cM) on chromosome 8. Eight SSR markers, YDS818, RM22984, RM22986, RM22997, YDS816, RM23002, RM339 and YDS810 completely co-segregated with the rpms1 gene. Another reverse PGMS gene (rpms2) was mapped to the interval between SSR markers RM23898 (0.9 cM) and YDS926 (0.9 cM) on chromosome 9. The physical mapping information from publicly available resources shows that the rpms1 and rpms2 loci are located in a region of 998 and 68 kb, respectively. The analysis based on marker genotypes showed that the effect of rpms1 was slightly larger than that of rpms2 and that the two genes interacted in controlling male sterility. H. F. Peng, Z. F. Zhang and B. Wu contributed equally to this work.     

利用染色体片段置换系定位水稻落粒性主效QTL

水稻落粒性是与其生产密切相关的重要性状之一。以7个染色体片段置换系为材料, 采用重叠群代换作图法对控制落粒性的2个主效QTL进行定位。结果表明, 104个SSR标记在亲本间具有多态性, 多态率为68.0%; 4个置换系的落粒性与亲本日本晴的落粒性相似, 表现难落粒。3个置换系与亲本93-11的落粒性相似, 表现易落粒; 7个染色体片段置换系在第1和第6染色体上检出7个置换片段, 其长度分别为23.6、16.5、 6.6、 9.9、 10.4、 20.2和7.1 cM; qSH-1-1被定位在第1染色体RM472－RM1387之间, 遗传距离约为6.6 cM。qSH-6-1为新发现的落粒性主效QTL, 被定位在第6染色体RM6782－RM3430之间,遗传距离约为4.2 cM。利用染色体片段置换系能准确地定位水稻落粒性QTL, qSH-1-1与qSH-6-1的鉴定和初步定位为其进一步的精细定位、图位克隆及分子标记辅助选择奠定了基础。     

一个控制水稻籽粒长度主效基因--Lk-4(t)的BC2F2群体定位及其遗传效应分析

水稻籽粒大小和形状是影响稻米外观品质和产量的重要影响因素,对控制这些性状基因的定位和克隆有助于弄清籽粒大小基因的表达模式和相应的代谢系统,最终实现该性状的自由调控。运用SSR和CAPs标记对来源于蜀恢527//蜀恢527／小粒回交组合BC2F2群体800隐性长粒单株进行分析,定位了一个控制水稻籽粒长短的基因,Lk-4（t）。对F2和BC2F2群体籽粒大小形状和千粒重的遗传分析表明,回交能将大部分对目的基因效应具有干扰修饰作用的微效基因多态性除去,从而有利于对目的基因型的准确鉴定;在F2和BC2F2群体中只发现两类籽粒长短表现型,即短粒和长粒,并且二者分离比例符合3：1的典型一对等位基因分离比例。这说明群体中籽粒长短变异是受一对基因控制。通过对BC2F2群体中隐性（长粒）单株进行分子标记分析,将这个控制籽粒长短的主效基因定位在3个CAPs标记,P1-EcoRV,P2-SacⅠ和P3-MboⅠ附近。连锁分析表明,Lk-4（t）位于水稻第3染色体着丝粒附近,离标记P1-EcoRⅤ和P2-SacⅠ分别有0．90cM和0．50cM的距离。     

Fine mapping of a grain weight quantitative trait locus on rice chromosome 8 using near-isogenic lines derived from a cross between Oryza sativa and Oryza rufipogon

A quantitative trait locus (QTL) for grain weight (GW) was detected near SSR marker RM210 on chromosome 8 in backcross populations derived from a cross between the Korean japonica cultivar Hwaseongbyeo and Oryza rufipogon (IRGC 105491). The O. rufipogon allele increased GW in the Hwaseongbyeo background despite the fact that O. rufipogon was the small-seeded parent. Using sister BC₃F₃ near-isogenic lines (NILs), gw8.1 was validated and mapped to a 6.1 cM region in the interval between RM42 and RM210 (P≤0.0001). Substitution mapping with eight BC₃F₄ sub-NILs further narrowed the interval containing gw8.1 to about 306.4 kb between markers RM23201.CNR151 and RM30000.CNR99. A yield trial using homozygous BC₃F₄ sister sub-NILs and the Hwaseongbyeo recurrent parent indicated that the NIL carrying an O. rufipogon chromosome segment across the entire gw8.1 target region out-yielded its sister NIL (containing Hwaseongbyeo chromosome in the RM42–RM210 interval) by 9% (P=0.029). The higher-yielding NIL produced 19.3% more grain than the Hwaseongbyeo recurrent parent (P=0.018). Analysis of a BC₃F₄ NIL indicated that the variation for GW is associated with variation in grain shape, specifically grain length. The locus, gw8.1 is of particular interest because of its independence from undesirable height and grain quality traits. SSR markers tightly linked to the GW QTL will facilitate cloning of the gene underlying this QTL as well as marker-assisted selection for variation in GW in an applied breeding program.     

Mapping of qGL7-2,a grain length QTL on chromosome 7 of rice

A residual heterozygous line(RHL)carrying a heterozygous segment between two SSR loci RM11 and RM134 on the rice chromosome 7 was selected from a set of recombinant inbred lines from the cross D50(javanica)/HB277(indica).The former parent produces much longer grains than the latter.Selfed progenies of this selection were analyzed genotypically(SSRs)and phenotypically(grain length).Grain length was discontinuously variable in the mapping populations,allowing for the placement of this QTL qGL7-2 within a～4.8 cM interval defined by RM351 and RM234.A set of new markers within this region were developed,which narrowed the QTL to a 278 kb region defined by the markers Indel1 and RM21945.This region contains 49 predicted genes.The results also suggest that the novel allele for grain length will be used for the application of marker assisted selection for the improvement of grain length.     

Fine mapping of a pistilloid-stamen (PS) gene on the short arm of chromosome 1 in rice.

A novel floral organ mutant of rice (Oryza sativa L. subsp. indica), termed pistilloid-stamen (ps) here, has flowers with degenerated lemma and palea, with some stamens transformed into pistils and pistil-stamen chimeras. Genetic analysis confirmed that the ps trait is controlled by a single recessive gene. F2 and F3 segregation populations derived from PS ps heterozygote crossed with Oryza sativa subsp. indica 'Luhui-17' (PS PS) were used for molecular mapping of the gene using simple sequence repeat (SSR) markers. With 97 recessive individuals from an F2 segregation population, the ps locus was preliminarily mapped 6.2 cM distal to marker RM6324 and 3.1 cM proximal to marker RM6340 in the terminal region of the short arm of chromosome 1. With a large F3 segregation population, the gene was fine-mapped between markers RM6470 and RM1141, at distances of 0.10 and 0.03 cM to each marker, respectively. The position of the ps gene was finally located within a 20 kb physical region containing 3 annotated putative genes. One of them, encoding a protein with a single C2H2 zinc-finger domain, may be the candidate gene for PS.     

一个新的水稻叶形突变体（tll1）的遗传分析与精细定位

利用甲基磺酸乙酯（ethylmethane sulphonate,EMS）诱变粳稻品种日本晴获得了一个遗传稳定的叶形突变体thread-like leaf1（tll1）。该突变体在杭州表现为矮化、窄叶,极端时仅剩主脉,呈细丝状。将该突变体分别与籼稻品种南京6号、浙辐802和9311进行正反交配组,遗传分析表明该突变体性状由1对隐性单基因控制。通过SSR和STS分子标记对F2代分离群体进行遗传定位,将该基因初步定位在第12染色体SSR标记RM247和RM101之间。随后利用已公布的粳稻品种日本晴和籼稻品种9311的基因组序列,发展了7对有多态的STS标记,最终将该基因定位在FL13和FL14之间约94.3kb的区间内,为进一步克隆TLL1基因奠定了基础。