Mapping of QTLs for leaf developmental behavior in rice (Oryza sativa L.)

Leaf developmental behavior in rice (Oryza sativa L.) is one of the important agronomic characteristics, which not only determines vegetative growth but also influences grain yield. This study was conducted to identify quantitative trait loci (QTLs) for total number of leaves (TNL), days to the emergence of flag-leaf (DEF) and the leaf emergence rates (LER) on main stem, which mainly represent leaf developmental behavior, using recombinant inbred lines (RILs) derived from a cross between a japonica variety, Asominori and an indica variety, IR24, cultivated in 2001 and 2002. The transgressive segregations in both parental directions and continuous variations of all three tested traits were observed. Significant correlations among these traits were detected. A total of fourteen QTLs for leaf development behavior were detected with 289 RFLP markers. Six QTLs controlling TNL were mapped to chromosomes 3, 5, 6, 8, 9, 12, and accounted for 5.615.7% of the total phenotypic variations, and three QTLs for DEF were mapped to chromosome 3, 6, 8 and accounted for 10.735.4% of total phenotype variation and five QTLs for LER were mapped to chromosome 1(two QTLs), 2, 4, 9 and explained 6.217.5% of phenotype variation. The identification of QTLs for leaf developmental behavior in rice may be useful for selection of fast growing genotype before heading using maker-assisted selection.     

基于CSSSLs的水稻穗长QTL的定位

穗长是影响水稻产量的重要因子之一,是典型的数量性状,遗传基础复杂,且易受环境等因素的影响。染色体单片段代换系(Chromosome single segment substitution lines,CSSSLs)减少了个体间遗传背景的干扰,是鉴定复杂性状QTL的新型遗传材料。本研究以广陆矮4号为受体、日本晴为供体的85个染色体单片段代换系群体为试验材料,通过单因素方差分析和Dunnett’s多重比较测验单片段代换系与受体亲本广陆矮4号之间穗长的差异,对代换片段上穗长QTL进行了鉴定。以P<0.001为阈值,共检测到22个穗长QTLs,分布于除第10染色体以外的11条染色体上,其加性效应值的变化范围为-2.63～3.87,加性效应百分率变化范围为-11.47%～16.88%。这些QTLs的鉴定,为进一步克隆穗长QTL以及水稻穗长的分子改良提供了重要的依据。     

Substitution mapping of QTLs for blast resistance with SSSLs in rice (Oryza sativa L.)

Rice blast, caused by fungal pathogen Magnaporthe grisea Barr., is one of the most devastating rice diseases worldwide. It has greatly affected the rice production and quality. Development of resistant cultivars is the most effective and economical way for controlling this disease in rice. In this study, 114 of the single-segment substitution lines (SSSLs) in rice were inoculated at seedling stage by 16 rice blast isolates. The substituted segments in the 114 SSSLs distributed on 12 chromosomes with coverage of 57.32% of rice genome. Fifteen of the SSSLs were different in blast resistance from the HJX74 recipient. The SSSL W23-7-6-5-2-2 showed 100% of resistance frequency. A total of 11 QTLs for blast resistance were detected on chromosomes 1, 2, 3, 6, 10, 11 and 12 in rice. They were mapped at chromosomal intervals of 2.2?C46.2?cM, of which 6 QTLs were mapped at less than 10.0?cM. Six of the 11 QTLs were first reported in this paper.     

Wide compatibility in rice (Oryza sativa L.)

Summary Wide compatible varieties (WCVs) show normal spikelet fertility in crosses with Indica and Japonica rice varieties. Crosses of Indica and Japonica varieties frequently show high spikelet sterility which prevents exploitation of heterosis for grain yield. We screened 41 rice varieties for the wide compatibility trait by crossing each with three Indica and three Japonica testers. Varieties giving fertile F₁ hybrids with both groups of testers were classified as WCVs. Seven varieties viz., BPI-76 (Indica); N 22; Lambayeque-1 and Dular (Aus); Moroberekan, Palawan and Fossa HV (Japonicas), were identified as WCVs. The frequency of WCVs was higher among Aus and Japonicas. The wide compatibility trait in varieties: Dular and Moroberekan was controlled by a single dominant gene linked with the Est-2 and Amp-3 loci (mean recombination 32.0%). Est-2 and Amp-3 showed complete linkage. Pgi-2 was found to be linked with Est-2 and Amp-3 (mean recombination 16.1%). Est-2 and Amp-3, showed a tighter linkage with C ⁺ (mean recombination 4.1%). Pgi-2 showed a lower linkage with C ⁺ (mean recombination 17.3%). The recombination values between the WC gene in Dular and C ⁺ was much higher than those reported in Japan for the WC gene (S₅ ⁿ) from Ketan Nangka. It is possible that the WC gene from Dular is different from that in Ketan Nangka. Linkage intensities with the WC gene were not strong enough to be of use for indirect selection for the wide compatibility trait. A search for a more closely linked isozyme or DNA marker was proposed.     

Fine mapping of stable QTLs related to eating quality in rice (Oryza sativa L.) by CSSLs harboring small target chromosomal segments

Amylose content (AC) and viscosity profile are primary indices for evaluating eating and cooking qualities of rice grain. Using chromosome segment substitution lines (CSSLs), previous studies identified a QTL cluster of genes for rice eating and cooking quality in the interval R727–G1149 on chromosome 8. In this study we report two QTLs for viscosity parameters, respectively controlling setback viscosity (SBV) and consistency viscosity (CSV), located in the same interval using rapid viscosity analyzer (RVA) profile as an indicator of eating quality. Previously reported QTL for AC was dissected into two components with opposite genetic effects. Of four QTLs, qCSV-8 and qAC-8-2 had stable genetic effects across three and four environments, respectively. qSBV-8, qCSV-8 and qAC-8-1 partly overlapped, but were separated from qAC-8-2. Based on data from an Affymetrix rice GeneChip, two genes related to starch biosynthesis at the qAC-8-2 locus were chosen for further quantitative expression analysis. Both genes showed enhanced expression in sub-CSSLs carrying the target qAC-8-2 allele, but not in sub-CSSLs without the target qAC-8-2 allele, indicating their possible role in rice quality determination. Molecular markers closely linked to the two stable QTL provide the opportunity for marker-assisted selection (MAS) in breeding high quality rice.     

利用4个姊妹近等基因系群体定位水稻粒重和粒形QTL

粒重是决定水稻产量的三要素之一。利用世界上粒重最大的品种之一SLG-1(供体亲本)与小粒品种日本晴(Nipponbare,轮回亲本)杂交,在各回交世代选择粒重较大单株与日本晴回交,构建水稻粒重和粒形的姊妹近等基因系(SNILs)。对获得的73株BC4F1单株进行粒重频率分布统计,选择粒重频率分布在4个峰值处的代表性单株,自交获得4个BC4F2SNILs群体。利用BSA法(分离群体分组混合分析法),从均匀分布在水稻染色体上的1513对SSR标记中筛选出与粒重和粒形相关的多态性标记19对,以LOD≥2.5作为选择阈值,对粒重、粒长、粒宽和粒厚进行QTL扫描,共检测到6个区域的12个QTL,贡献率从7.22%到53.38%。这些QTL所在区域包含已克隆的粒长GS3和粒宽GW2,也包含没有精细定位的第2染色体的RM6318～RM1367、第3染色体的RM5477～RM6417和第6染色体的RM3370～RM1161等3个区域控制粒重和粒形的5个QTL。其中第3染色体上RM5477～RM6417区间存在粒形贡献率较大的新的QTL。构建含有这些粒重QTL的姊妹近等基因系,为进一步精细定位或克隆新的粒重或粒形QTL奠定了基础。     

水稻单片段替换系群体的建立及QTL定位

水稻中许多重要的农艺性状属数量性状,由多基因(QTL)控制。研究QTL的遗传特性和遗传效应对于培育高产和稳产的水稻品种具有十分重要的意义。本研究以6个优良的品种为供体亲本,以华粳籼74为轮回亲本,通过微卫星标记辅助回交选择培育了一批单片段替换系,随后利用所培育的单片段替换系进行了QTL分析和基因定位。主要结果有：1、利用258个微卫星标记对6个供体亲本和轮回亲本间的多态性进行了筛选。6个供体亲本与轮回亲本间的多态率在32．98％至60．78％之间,平均47．81％,粳型供体亲本比籼型供体亲本的多态性要高。2、随着回交代数的增加,植株所含的替换片段数逐渐减少。在BC2F1、BC3F1、BC3F2和BC3F3代,平均每个植株携带有12．50、5．98、1．69和1．46个替换片段。替换片段的平均长度也随回交和自交代数的增加而逐渐变短。在BC2F1、BC3F1、BC3F2和BC3F3代,替换片段的平均长度分别为25．43cM、22．38cM、20．78cM和18．15cM.回交世代替换片段变短的速率(11．99％)比自交世代变短速率(7．15％)要快。在BC2F1、BC3Fl、BC3F2和BC3F3代,轮回亲本基因组的恢复率分别为82．24％、92．55％、98．04％j阳98．52％。3、在BC3F2和BC3F3代,共选育出111个单片段替换系,其中独一无二的单片段替换系共42个。BC3F2代替换系中替换片段的估算长度在2．00cM到64．80cM之间,平均为21．75cM,而BC3F3代中替换片段的估算长度在6．05cM到48．90cM之间,平均为20．95cMc,12条染色体中仅第11染色体没有选择到单片段替换系。所选育的单片段替换系中替换片段的总长为2367．50cM,基因组的覆盖长度为704．50cM,覆盖率为39．25％。4、在52个单片段替换系的22个性状中共鉴定出了234个QTL。每个性状鉴定出的QTL数在3到19个之间,平均4．50个。每个替换系鉴定出的QTL在2到15个之间,平均10．64个。QTL加性效应的大小因性状和替换系不同而不同,低至-0．02(0．79％)的加性效应(如谷粒宽度)均能检测到。在RM237．RM322、RM225和RM481标记附近的各种性状中同时检测到了增效和减效的QTL。5、通过染色体替换作图,对7个单片段替换系中16个性状的QTL进行了定位。利用携带有相同替换片段的替换系进行QTL位置的确定。6、通过分析复杂性状的加性效应,对影响植高、每穗粒数和粒型的相关性状进行了分析,分析QTL之间的相关性。7、对控制抽穗期、稃尖颜色、植株高度和粒型的基因进行了定位。抽穗期基因Hd-8表现为单基因显性遗传,定位于第8染色体上,与PSMl55紧密连锁。紫色稃尖基因Pa-6表现为单基因显性遗传,定位于第6染色体上,与RM253紧密连锁。株高基因Ph-1-3定位于第1染色体上,与PSM331紧密连锁。粒型基因Rlw-8-2为首次报道,定位于第8染色体的末端,与RM447紧密连锁,长粒表现为单基因隐性遗传。本研究通过分子标记辅助选择培育了一批单片段替换系,并成功地对这批材料进行了QTL分析和基因定位,从而证实了在水稻中通过微卫星标记辅助回交选育单片段替换系和进行QTL分析的可行性。     

Inheritance of amylose content in rice (Oryza sativa L.)

Summary The inheritance of low and very low amylose contents in six rice crosses and their reciprocals was studied by single grain analysis of parents F₁, F₂, B₁ and B₂ seeds. To minimize the environmental effects, the seeds of all generations of all crosses were produced in a single season. The results indicated different dosage effects in different crosses. One major gene was found to govern a difference of 6–12% in amylose content in low and intermediate amylose parents. Very low amylose content was similarly found to be governed by one major gene in crosses between very low- and low-amylose content parents. Minor genes and modifiers also seem to play some role. In the cross between two low amylose parents differing by about 2.5% in amylose content, the differences appeared to be controlled by some minor genes and modifiers. The selection program in different crosses has been suggested.     

籼粳交稻米品质性状杂种优势的遗传分析

用胚乳性状遗传模型和分析方法对籼粳交稻米品质性状的杂种优势进行了遗传分析,结果表明：各品质性状都具有一定的杂种优势,其中碱消值和蛋白质含量的优势较强。直链淀粉含量和胶稠度的优势较弱。不同性状杂种优势的遗传原因不同,直接显性和母体显性对杂种优势的贡献大小因性状而异,但总的来说,母体显性对籼粳杂种Ｆ２籽粒品质性状的杂种优势具有重要的意义,细胞质效应对部分性状（如胶稠度、蛋白质含量）的群体平均优势有一定     

A study on heterosis in rice (Oryza sativa L.)

Summary Heterosis for yield and four yield components, viz. panicle number per plant, panicle length, spikelet per panicle and 1000-grain weight, was studied in fifteen crosses involving six varieties of rice, Oryza sativa L. Positive and significant heterosis for yield was observed in 11 and 8 crosses, over the mid-parent and the better parent, respectively. Hamsa x Hybrid 27 gave the highest heterosis both over the mid-parent (156.23%) and the better parent (136.38%) followed by Jaya x Norin 18 with respective values of 155.18 and 56.29%.As compared with the average yield of 36.54 g per plant of the high yielding commercial variety, viz. Jaya hybrids in 8 crosses gave significant higher yield and four crosses, viz. Hamsa x Hybrid 27, Hybrid 27 x Jhona 349, Jaya x Palman 579 and Jaya x Hybrid 27, gave 80.51, 66.56, 57.11 and 56.30 g per plant, recording an increase of 120.33, 82.13, 56.29 and 54.08%, respectively. The heterosis for yield was due to simultaneous heterosis for a number of yield components. The possibility of hybrid crop production as compared with the recently developed high yielding rice varieties has also been discussed.Contribution No. 73.15 from the Department of Plant Breeding, Punjab Agricultural University, Ludhiana, India.     

Linkage of genes for anthocyanin pigmentation in rice (Oryza sativa L.)

Summary The inheritance of anthocyanin pigmentation and the interrelationship between genes governing anthocyanin pigmentation in different parts of the rice plant and genes governing panicle density were studied in the cross Suma × Wanar-1. A ratio of 45 pigmented: 19 non pigmented was realised for anthocyanin accumulation in sheath, nodal ring, internode, leaf tip, leaf margin and apiculus whereas a ratio of 3 normal:1 laxy was observed for panicle density. Pleiotropic action of a basic gene (A) and each of the two complementary duplicate genes (P _a or P _b) was detected. A linkage group of genes localising pigment in six plant parts was identified, the sequence of genes being P _nr-P _lm-P _la-P _a-P _sh-P _in. This may form part of the III S _p group of Misro et al. (1966), in which case the genes P _nr and P _la are proposed to be additions to this group.     

Mapping of quantitative trait loci controlling seedling vigor in rice (Oryza sativa L.) under submergence

Submergence-induced suppression of seedling vigor is a serious constraint particularly in the direct seeding rice cultivation system. To identify quantitative trait loci (QTLs) associated with seedling vigor in rice under submergence, a mapping population of 98 Backcross Inbred Lines derived from a cross of Nipponbare/Kasalath//Nipponbare was used. Phenotypic evaluation of seedling vigor under submergence was based on shoot length (SHL), root length (RTL) and shoot fresh weight (SFW) using a test tube bioassay method. Thirty-two putative QTLs were detected among which 7 were for SHL, 11 for RTL and 14 for SFW. Phenotypic evaluation was also made of the parental lines and a set of 54 chromosome segment substitution lines in which Nipponbare segments were substituted for by their homologous Kasalath segments covering the entire rice genome. Two QTLs with more than 10 % contribution to the total phenotypic variance were verified for SHL, and at least one for RTL and six for SFW on chromosomes 1, 3, 4, 6 and 7 at the 1 % significance level. Among these, all but two showed reductions in one, two or all three traits. Our present and previous results suggest that the Nipponbare genome has a potential to improve seedling vigor under submergence and that japonica germplasms can be used to breed for this important trait in indica rice.     

QTL analysis of seed dormancy in rice (Oryza sativa L.)

Effective cumulative temperature (ECT) after heading would be a more reasonable parameter for seed sampling of pre-harvest sprouting/seed dormancy (SD) tests in segregating populations than the days after flowering. SD is an important agronomic trait associated with grain yielding, eating quality and seed quality. To identify genomic regions affecting SD at different grain-filling temperatures, and to further examine the association between SD and ECT during grain-filling, 127 double haploid (DH) lines derived from a cross between ZYQ8 (indica)/JX17 (japonica) by anther culture were analyzed. The quantitative trait loci (QTLs) and their digenic epistasis for SD were identified using a molecular linkage map of this population. A total of four putative QTLs for SD (qSD-3, qSD-5, 6 and 11) were detected on chromosomes 3, 5, 6 and 11, together explaining 41.4% of the phenotypic variation. Nine pairs of digenic epistatic loci were associated with SD on all but chromosome 9, and their contributions to phenotypic variation varied from 2.87%–8.73%. The SD QTL on chromosome 3 was identical to the QTLs found in other mapping populations with different genetic backgrounds, which could be a desirable candidate for gene cloning and marker-assisted selection in rice breeding.     

Anther and pollen grain culture of rice (Oryza sativa L.)

Summary Factors favouring callus proliferation and subsequent regeneration of plants from pollen grains of rice anthers (Oryza sativa L., cvx. Bahia, Girona, Balilla × Sollana and Sequial) were determined. Cultivar differences in response were found, such as a high rate of haploid plant regeneration.In addition, isolated pollen grain culture was used to induce tissue proliferation outside the anther walls. The frequency of callus formation from isolated pollen grains was very low. It was necessary to preculture the anthers before pollen grain separation, in order to accomplish a successful development later. Root differentiation was observed in some of the obtained callus.     

Genetics of stem elongation ability in rice (Oryza sativa L.)

Summary The genetics of stem elongation ability in rice was studied in parents, F₁, F₂ and backcross generations of six crosses. Segregation analysis indicated dominance for stem elongation ability. Estimation of genetic parameters under epistatic model indicated more than one locus control stem elongation ability and both additive and nonadditive gene effects were important. Epistatic effects were predominant over additive and dominance effects with an important role of duplicate type of epistasis. The occurrence of significant additive and additive x additive types of genetic variation and the moderately high broad sense heritability indicated the possibility of selection for an increased manifestation of stem elongation ability.     

Genetic analysis of ratooning ability of rice (Oryza sativa L.)

Summary Genetic analysis of generation means of F₁, F₂, F₃, F₄, and the parental populations of the cross IR10154-23-3-3A/IR15795-232-3-3-2 for ratooning ability was conducted. Good ratooning ability is a recessive trait. The parents differed by at least two pairs of major genes for ratooning ability. A large proportion of transgressive segregants in F₂ suggested that the expression of ratooning ability is influenced not only by major genes but also by modifiers. Broad-sense heritability estimates computed by different methods ranged from 0.66 to 0.88. Narrow-sense heritability by the F₄–F₃ regression method was 0.39. The heritability estimates were 0.42 and 0.33 by the variance component method. The prevalence of additive x additive type of gene effects along with prominent additive effects imply some scope for selection in the segregating generations. However, non-additive type of gene action also affects the expression of ratooning ability.     

A major gene for low temperature germinability in rice (Oryza sativa L.)

Low temperature-induced retardation of seedling growth is a common problem in temperate rice-growing areas, at high altitudes of tropical and sub-tropical areas, and in areas with a cold irrigation water supply. Studies on low temperature germinability have revealed complex inheritance of the trait. The purpose of this study was to identify the gene(s) for low temperature germinability using Italica Livorno as a donor parent. The frequency distributions for the germination rate at 15 °C in the F₂ and BC₁F₁ populations showed continuous segregation, suggesting that low temperature germinability was under polygenic control. Since some lines in the BC₁F₁ population showed vigorous low temperature germinability similar to that of Italica Livorno, backcrosses until the BC₅F₁ generation was carried out using Hayamasari as the recurrent parent. Clear segregations of low temperature germinability were observed in the BC₅F₁ and BC₅F₂ populations. The distribution of low temperature germinability fitted a single-gene segregation, indicating that a single dominant gene with a large effect was transferred to Hayamasari. This gene is tentatively symbolized as Ltg(t). Low temperature germinability of near isogenic lines for Ltg(t) was similar to that of Italica Livorno. Ltg(t) should greatly contribute to the improvement and manipulation of low temperature germinability in rice breeding programs. This revised version was published online in August 2006 with corrections to the Cover Date.