Genetic analysis of semidwarf mutants induced in indica rice (Oryza sativa L.)

The mode of inheritance of five semidwarf (SD) mutants and allelic relationship with DGWG (sd1) locus was studied. The five SD mutants viz., Basmati 370 (SD1), Basmati 370 (SD2), Basmati 370 (SD3), TCA 2 (SD) and TCA P2-5 (SD) when crossed with their tall parents exhibited monogenic inheritance of 3 tall: 1 semidwarf in the F2 progenies. The SD mutants were also crossed with semidwarf varieties (DGWG and Bala) possessing sd1 gene. Crosses between Basmati 370 (SD1) × Bala, Basmati 370 (SD3) × Bala and TCA 2 (SD) × DGWG produced tall F1 hybrids and in F2 generation, modified dihybrid ratios (9 : 6 : 1 and 9 : 7) were observed indicating that the mutants Basmati 370 (SD1), Basmati 370 (SD3) and TCA 2 (SD) are non-allelic to sd1 gene. Whereas, the mutants Basmati 370 (SD2) and TCA P2-5 (SD) when crossed with Bala produced semidwarf F1 hybrids and in F2 generation, segregation for plant height was not observed indicating that these mutants are allelic to sd1 gene. The three non-allelic SD mutants identified in the present study can be used in rice breeding as alternative gene sources for semidwarfism. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular mapping of a new genic male-sterility gene causing chalky endosperm in rice ( Oryza sativa L.)

A genic male-sterility gene newly induced by chemical mutagenesis, tentatively designated as ms-h(t), was located on the molecular map of rice and tested for its effect on chalky endosperm. Bulked segregant analysis was used to determine the chromosomal location of the ms-h(t) locus by screening four to five RFLP markers per chromosome. After confirming that the gene was located on chromosome 9, twenty-four RFLP markers from chromosome 9 were surveyed for polymorphism in the parents of the mapping population. Of these, eleven markers were mapped around the ms- h(t) locus. RG451 and RZ404 flanked the ms-h(t) gene, at 2.5cM and 3.3cM, respectively. Heterozygous F2 to F4 progenies were tested for co- segregation of male-sterility and chalky endosperm and it was revealed that ms-h(t) might have a pleiotropic effect on chalky endosperm. This mutant would be a good biological material to characterize the biochemical mechanism of male sterility and related pleiotropic effects. Further studies should be needed to know the usefulness of this mutant for hybrid seed production. This revised version was published online in July 2006 with corrections to the Cover Date.     

水稻圆粒基因RS的鉴定和定位

阐明水稻籽粒大小相关基因的遗传和分子机制对水稻产量形成具有重要意义。利用甲基磺酸乙酯(ethyl methanesulfonate, EMS)诱变粳稻品种宁粳3号筛选获得圆粒突变体round seed (rs)。遗传分析表明,突变体rs圆粒表型由单隐性核基因控制。颖壳扫描电镜观察发现,rs籽粒变圆主要是细胞数目改变导致的。在突变体rs中,细胞周期相关基因的表达较野生型显著升高。将RS定位在第3染色体短臂标记RM3413与N3-5之间,物理距离约589 kb。RS突变影响BR信号途径,改变了粒型相关基因的表达。本研究有助于阐明水稻籽粒发育的分子机制。     

Genetics of Panicle Exsertion in Cold-Tolerant Rice (Oryza sativa)

Four cold-tolerant rice varieties, viz. ‘Khonorullo’, ‘Namyi’, ‘Abor B’ and ‘Meghalaya-1’ were crossed with two cold-susceptible ones, viz. ‘Pusa 33’ and ‘Subhadra’ (DR92), in all possible combinations to study the inheritance of gene(s) governing panicle exsertion and their allelic relationship among cold-tolerant varieties. F₁ hybrids of all the crosses showed complete panicle exsertion indicating dominance of this trait. Segregation pattern of panicle exsertion in F₂ and backcrosses show that all the four cold-tolerant varieties possessed a single dominant gene designated as Ctr-1. Absence of segregation for panicle exsertion in an F₂ generation obtained from intercrosses of cold-tolerant varieties suggests that the dominant genes in all the four cultivars are allelic.     

Trisomic analysis of a strong photoperiod-sensitivity gene E1 in rice (Oryza sativa L.)

Recent genetic analyses on heading-time of rice indicated that almost all the well-adapted varieties in the temperate zone carry a strong photoperiod-sensitivity gene E1, a dominant allele of E1 locus. In order to identify the chromosome on which E1 is located, a trisomic analysis was made using two primary trisomic series originating from the japonica varieties, Nipponbare and Kinmaze, respectively. The Nipponbare and Kinmaze series were crossed with heading-time tester lines, EG0 and EG3, respectively, both of which did not carry the E1. The F2 populations for chromosome 1, 2, and 3 could not be analyzed due to lack of seed. All the other F2 populations showed distinct segregation into early-type and late-type plants caused by the E1 locus segregation, which suggested that the trisomic analysis for E1 locus could be efficiently made. Both disomic and trisomic groups in the F2 population from the cross of the trisomic line for chromosome 7 × EG0 showed a segregation ratio significantly different at the 1% level from a ratio of 1 [e1e1; early]: 3 [E1e1, E1E1; late]. This suggested that E1 was located on chromosome 7. Subsequently, the linkage analysis was made using three morphological marker genes on chromosome 7. It was recognized that E1 was linked to rfs (rolled fine strip gene) and slg (slender glume gene) with recombination values of 16.3 ± 5.88 and 9.1 ± 4.72%, respectively. From these results, it can be concluded that E1 is most likely to be located on chromosome 7. This revised version was published online in July 2006 with corrections to the Cover Date.     

水稻类病斑早衰突变体lmps1的表型鉴定与基因定位

经甲基磺酸乙酯(EMS)诱变优良籼型水稻恢复系缙恢10号,获得一个稳定遗传的水稻类病斑早衰突变体lmps1(lesion mimic and premature senescence 1)。该突变体苗期表型正常,分蘖早期出现褐色类病斑,且斑点数目随植株生长而增多,孕穗期叶片开始萎黄衰老。与野生型相比,突变体lmps1的每穗总粒数下降8%(P0.05),株高、穗长、有效穗数、每穗实粒数、结实率以及千粒重分别下降14.3%、24.3%、27.2%、50%、45.7%与14.5%,差异均达极显著水平(P0.01)。遮光处理表明,突变体lmps1的类病斑性状受光照诱导。孕穗期叶片光合色素含量下降且光合效率降低, H2O2含量增加,抗氧化酶SOD和CAT的活性显著降低。透射电镜观察结果显示,突变体lmps1叶肉细胞中叶绿体数目减少,叶绿体的类囊体片层结构损伤降解。qRT-PCR结果显示,突变体lmps1中防卫反应相关基因除POX22.3表达量降低外,POC1、PAL、PBZ1、PR1、NPR1、PR5表达量均极显著高于野生型。遗传分析表明突变体lmps1的类病斑早衰性状受1对隐性核基因控制,利用西农1A与突变体lmps1杂交所得F2群体中的突变株,将目标基因定位于第7染色体长臂端粒附近约167.3 kb的物理区段内。     

水稻半外卷叶突变体sol1的表型分析与基因定位

适度卷曲有利于提高水稻叶片的光合效率,增加植株光合产物的有效积累量。我们利用甲基磺酸乙酯(EMS)处理籼型水稻保持系西农1B,获得一个稳定遗传的水稻半外卷叶突变体。该突变体从十叶期开始各叶片逐渐向外卷曲直至半卷状,并伴随茎秆半矮化和叶片披垂,暂被命名为semi-outcurved leaf 1 (sol1)。与野生型(WT)相比, sol1的叶片卷曲指数均达到30%以上(P<0.01);倒一、倒二、倒三、倒四节节间长度和穗长极显著缩短,倒一、倒二、倒三叶的叶夹角显著或极显著增加;有效穗数、千粒重、每穗实粒数、结实率显著或极显著下降,一次枝梗数则增加11.3%(P<0.05)。sol1的蒸腾速率、胞间CO2浓度、气孔导度显著高于野生型。石蜡切片显示, sol1倒一叶的泡状细胞体积变小,数量显著增多,表皮细胞体积略微增大。遗传分析表明, sol1的半外卷叶性状受1对隐性核基因调控,定位于6号染色体标记JY6-3和JY6-10之间165kb的物理范围内,共含15个注释基因。qRT-PCR结果表明,与泡状细胞相关的内卷基因和外卷叶基因RL14、Roc5、REL1在突变体sol1中呈...     

Characterizations and molecular mapping of a novel dominant semi-dwarf gene Sdd(t) in rice (Oryza sativa)

By nitrogen ion implanting, we obtained a semi‐dwarf mutant from a japonica rice cultivar Y98148, designated as Y98149. The genetic analysis of Y98149 indicated that the semi‐dwarf phenotype was controlled by a single dominant gene, Sdd(t). We show that Y98149 reduced plant height mainly via inhibiting the first, second and third internode elongation. Based on this dwarfing pattern, the mutant could be grouped into dn‐type dwarf defined by Takeda [Gamma Field Symp. (1977) Vol. 16, PP. 1–18] . In addition, the Sdd(t) gene was sensitive to gibberellin (GA) based on the response to extraneous GA₃ and the quantitative determination of endogenous GA₁ and GA₄. To map the Sdd(t) gene, we tested molecular markers by bulk segregant analysis. The Sdd(t) gene was localized to a 6.4 cM‐interval on the short arm of chromosome 6, flanked by two sequence‐tagged site markers S9 and S13.     

水稻温敏型叶片白化转绿突变体tsa2的表型鉴定与基因定位

水稻温敏型叶色突变体是研究植物光合作用、叶绿体结构和功能以及温度影响叶绿体发育的理想材料。利用甲基磺酸乙酯(EMS)诱变籼型水稻(OryzasativaL.)三系保持系西农1B,从其后代中筛选到一个突变性状稳定遗传的温敏型叶片白化转绿突变体tsa2 (temperature-sensitive green-revertible albino 2)。与野生型相比, tsa2突变表型受温度影响, 22°C条件下萌发的野生型幼苗表型正常,而tsa2幼苗完全白化,且约40%白化苗死亡,存活白化苗的光合色素含量、光合速率均显著降低,成熟期主要农艺性状均显著变劣;在28°C下萌发的tsa2幼苗叶片呈浅绿色并伴有白条纹,其光合色素含量显著降低,光合速率及主要农艺性状差异较小; 32°C下萌发的tsa2幼苗叶片无明显差异。透射电镜观察显示,与野生型相比,tsa2在22°C下叶肉细胞中无叶绿体或存在异常发育叶绿体(尚未分化出基粒和基层),在28°C下部分叶肉细胞含少量发育完整的叶绿体,在32°C下叶肉细胞数量及形态均正常。实时荧光定量PCR(qRT-PCR)分析表明,与野生型相比,tsa2突变体中部分光合色素代谢途径基因、叶绿体发育相关基因及光合作用相关基因的表达水平呈不同程度变化。遗传分析表明, tsa2突变表型受一对隐性核基因控制, TSA2被定位于第5染色体SSR标记S5-57和S5-119之间,物理距离为718 kb。本研究为水稻遗传改良及研究温度影响叶绿体发育机制奠定了基础。     

High-lysine mutants of rice, Oryza sativa L.

In order to improve the nutritive value of rice protein, it is necessary to increase the level of lysine and threonine. Ten high-lysine mutants were selected from N-methyl-N-nitrosourea-induced (MNU-induced) mutant lines, using high-performance liquid chromatography for amino acid analysis. The lysine content of these mutants ranged from 5.10% to 6.38% of total amino acids, while that of the original varieties was about 4%. All high-lysine mutants also had a greatly increased histidine content and a floury endosperm. An increase in lysine content of the albumin/globulin fraction was characteristic of the MNU-induced high-lysine mutants. The segregation ratio of normal to floury endosperm in the F2 seeds from a cross between ‘Kinmaze’ and a high-lysine mutant fitted the expected 3:1 ratio. The high level of lysine and the floury endosperm may be controlled by the same gene.     

AMMI analysis of rainfed lowland rice (Oryza sativa) trials in Nigeria

The additive main effects and multiplicative interaction (AMMI) model is used to analyse the grain yield data of 13 rice genotypes grown in 12 rainfed lowland rice environments. The trials were organized by the International Network for Genetic Evaluation of Rice in Africa (INGER-Africa) and conducted in Nigeria. Main effects due to environments (E), genotypes (G) and G × E interaction were found to be significant (P = 0.001). Cross validation analysis suggested that an AMMI model with one interaction principal component axis (IPCA) was most useful predictively, whereas Gollobs’ test declared two components, IPCA1 and IPCA2, statistically significant (P = 0.01). The IPCAl, however, accounted for most (47.8%) of the G × E sum of squares. Correlation and regression analysis, and relative scatter of genotype and environment points on the AMMI biplot suggest that the interaction partitioned in IPCA1 resulted from differences in the days to flowering among the genotypes. The paper discusses these in relation to the occurrence of Fe toxicity at the test sites and varietal tolerance to the stress.     

Fine mapping and photosynthetic characteristics of the lower chlorophyll b 1 mutant in rice (Oryza sativa L.)

Chlorophylls absorb and transfer light energy to the photosynthetic system. Consequently, chlorophyll content is strongly related to crop biomass and yield. We isolated a rice spontaneous mutant, lower chlorophyll b 1 (lcb1), from a recombinant inbred line population. Under normal growth conditions, lcb1 plants produced yellow leaves with decreased total chlorophyll and chlorophyll b contents, but normal chlorophyll a content. Photosynthetic and fluorescence parameters differed between wild‐type and lcb1 plants. Compared with wild type, lcb1 had a higher electron transfer rate, a lower photochemical quenching coefficient and significantly reduced grain number, biomass and yield. A recessive nuclear gene controlled the mutant trait. Through map‐based cloning, we located the LCB1 gene in a 117.4‐kb region on the short arm of chromosome 3, close to the centromere, in a region containing 15 predicted candidate genes. None of these genes was directly related to chlorophylls or the chloroplast; therefore, lcb1 may be a mutation of a novel gene. These results will be useful for further research on the molecular mechanisms controlling biogenesis and chloroplast biochemical processes.     

Genetic analysis and fine mapping of a dominant dwarfness gene from wild rice (Oryza barthii)

Plant architecture has been proposed as a means to enhance the potential yield of rice, especially by reducing height to provide lodging resistance. In this study, we developed a near‐isogenic line (NIL) using cultivar ‘Dianjingyou 1’ (DJY1) as a recipient parent and wild rice (Oryza barthii) as the donor parent. The NIL had semi‐dwarf stature and more tillers than DJY1. Cytological examination showed decreased numbers of cells in the stems of the NIL compared to DJY1. Genetic analysis indicated that this phenotype was controlled by a newly identified dominant dwarf gene, tentatively named as Dd7. A large population derived from the hybrid NIL‐Dd7/DJY1 was developed to fine‐map Dd7. Based on the physical location of molecular markers, the Dd7 locus was finally delimited to an 82‐kb region in chromosome 7. Gene prediction identified 14 open reading frames (ORFs) within this region. NIL‐Dd7 seems to confer no undesirable pleiotropic effects and therefore has potential value for rice breeding.     

Semidwarf gene sdk has pleiotropic effects on rice (Oryza sativa L.) plant architecture

Ideal plant architecture has become a significant objective in high‐yield rice breeding. In this study, a new semidwarf gene in sdk, a spontaneous dwarf mutant of ‘Kasalath’, was characterized and genetically mapped. The mutant has smaller panicles and seeds, reduced awns, and is 6–8 days earlier in heading than ‘Kasalath’. There was no significant difference in number (No.) of seeds and fertile seeds per panicle. Genetic analysis indicated that the dwarf character of sdk is controlled by a recessive gene, semidwarf k (sdk). From a segregating population of about 65 000 individuals, 4987 sdk‐type individuals were sampled. Gene sdk was located in a genomic region of 2622 kb flanked by markers R‐12 and R‐43 in the centromeric region of chromosome 2. The results provide an opportunity for gaining an understanding of the molecular mechanisms underlying sdk and opening possibilities for its use in rice breeding programmes.     

QTL analysis for resistance to preharvest sprouting in rice (Oryza sativa)

Preharvest sprouting (PHS) is caused by early breaking of seed dormancy. In Sichuan, a major hybrid rice seed production area of China, PHS in hybrid seeds originated from ‘G46A’ parent may lead to severe yield loss, causing serious damage to agricultural production. To detect quantitative trait loci (QTLs) governing PHS, we developed an F₂ population of 164 plants derived from ‘G46B’ and ‘K81’, a near‐isogenic introgression line of G46B, with high level of resistance to PHS. PHS was evaluated under controlled field and laboratory conditions. Using simple sequence repeat markers, we constructed a linkage map from this population and identified three QTLs for PHS, namely qPSR2, qPSR5 and qPSR8, which were located on chromosomes 2, 5 and 8, respectively. Among these QTLs, qPSR8, residing in the interval between RM447 and RM3754 on chromosome 8, was the major QTL controlling PHS, for it had a relative high logarithm of the odds (LOD) score and explained 43.04% of the phenotypic variation. These results were correspondent to those identified in extreme low germination rate plants (ELGP) using linkage and linkage disequilibrium. At all loci, ‘K81’ was responsible for enhancing the resistance to PHS.     

Complex constitutive nature of Japanese upland rice, Oryza sativa L.

Two rice ecotypes, the so-called lowland and upland populations, which carry different isozyme genotypes mostly at a single locus, are cultivated in Japan. The aim of this study was to examine the origin and the mechanism for keeping these genetic differences. The upland population is cultivated in upland fields and carries a different allele for a particular isozyme gene, Pgd-1, which has never been found in the lowland population. RFLP markers showed a weak trend for genetic differentiation between the two ecotypes. On the other hand, morphological, and physiological traits showed marked differences between the two ecotypes. Furthermore, based on the genotypic difference, two Japonica subgroups are defined in the upland population. Subgroup I is the minor group and carries key lowland characters, including the genotype for PGD. Subgroup II carries different traits and the genotype for PGD of the alternative subgroup. As an allelic difference for Pgd-1 is known to occur between the two ecospecies, Tropical (Tr) and Temperate (Tm) Japonicas, upland cultivars can be classified by diagnostic characters which distinguish a variety into Tr or Tm type. The upland population consists of three types of cultivars, Tr-, Tm- and intermediate-type. In contrast, the lowland population consists of a uniform Tm type Japonicas. As Japanese upland cultivars still have an isozyme allele specific to the Tr type, the upland population has a rather complex constitution which is presumably now being introgressed by lowland genetic material, but still represents a major difference at some genetic levels. Upland rice carries several stress-resistant genes which would be useful for lowland rice breeding. The genetic difference would be efficient for tagging upland specific traits by upland specific genetic markers. This revised version was published online in July 2006 with corrections to the Cover Date.     

Identification of quantitative trait loci underlying milling quality of rice (Oryza sativa) grains

Milling quality of rice grains is important to both producers and consumers. In this study, quantitative trait loci (QTLs) controlling brown rice rate (BR), milled rice recovery (MR) and head rice recovery (HR) were analysed by composite interval mapping over 2 years using 98 backcross inbred lines (BILs). A total of 12 QTLs for the three traits were detected, of which five were for BR, four for MR and three for HR. The proportion of phenotypic variation explained by individual QTLs ranged from 7.5 to 19.9%, and additive effects contributed by a single QTL accounted for 0.46 to 2.34% of the variation. QTL‐by‐environment interactions were observed by comparing QTL mapping of the same population grown in two consecutive years. Three of five QTLs for BR and two of four QTLs for MR were detected in 2 years, and all three QTLs for HR were detected in 1 year only. BR was significantly correlated with MR, and all four QTLs of MR were located in the same regions as those of BR. This indicated that QTLs for highly correlated traits could often be detected in the same interval.     

Variation among progenies of diploid plants regenerated from haploid, microspore-derived cell-suspension protoplasts of rice (Oryza sativa L.)

Progenies of 110 diploid R₀ plants regenerated from haploid protoplasts derived from microspore callus cell suspension culture of rice (cv. Miara) were evaluated for 6 traits, along with control lines, in a replicated field trial. Complementary post-harvest observations were carried out for four panicle or grain characters. A wide range of variation was observed for all traits under study among the protoclonal lines. The mean of the protoclonal population was significantly different from that of the control for most traits and 64.5% of the lines differed from the control for at least one field-evaluated trait. A unidirectional shift towards later-maturing, taller, and lower-tillering lines was observed. Of all the lines, 39% were taller than the control by at least 10 cm, 31 % had flowering delayed by at least 5 days, and 13% exhibited significantly longer panicles (P = 0.05). As to the agronomical value of the lines, the variation resulted in a global negative drift although favourable variations were found in a few lines. All but two lines were homogeneous, suggesting that most variations existed in a homozygous form in the R₀ plants. R₂ lines grown from seeds of 17 R₁ protoclonal lines stably inherited the changes and did not segregate, thereby confirming that variations are fixed.