Estimation of the outcrossing rate for annual Asian wild rice under field conditions

The Asian wild rice, Oryza rufipogon, has partial outcrossing behavior and shows high levels of genetic variation. To estimate an accurate outcrossing rate of annual form of O. rufipogon, two backcross lines (Lines R1 and R2) between Oryza sativa Nipponbare and O. rufipogon W630 were examined under field conditions. A chromosome survey confirmed that these lines had wild chromosomal segments at more than 92% of marker loci. As for the traits of glume, stamen and pistil, Line R1 showed similar floral morphology as that of O. rufipogon W630, whereas Line R2 had larger glumes. In 2005, 2006 and 2008, a total of 22 backcross plants were planted in the middle of wild rice plots. The successive progenies of each plant were examined using microsatellite markers that could clearly detect self-pollination and outcrossing. The outcrossing rates of Line R1 plants ranged from 4.04% to 25.50% with an average of 10.20%. This indicates that cross-pollination of wild rice is a chance event affected by many environmental factors. The outcrossing rates of Line R2 plants also varied, however, no significant difference was observed between the averages of Lines R1 and R2, suggesting that the glume sizes are not critical for outcrossing ability.     

Variation of the vascular bundle system in Asian wild rice, Oryza rufipogon and its relationship to rachis branch number and growth habit

Accessions of Asian wild rice, Oryza rufipogonGriff., vary in phenology, growth habit, reproductivesystem, panicle architecture and rachis branchnumbers, and in habitat preferences. In this paper 86accessions of annual, perennial and intermediategrowth habit variants have been examined for variationin the numbers of rachis branches in the panicle andvascular bundles in their subtending peduncles.Accessions of annual habit, which regenerate from seedand are adapted to shallow and temporary swamps,developed fewer rachis branches (mean = 6.0) thanthose of perennial habit (mean = 7.2) which largelyregenerate vegetatively and are adapted to stable deepwater habits. In both cases variation within growthhabit groupings was narrow. Variation in vascularbundle numbers, which has not been previouslyreported, was similar (10.1 to 10.3), but morevariable within annuals. As a result the V/R ratio (ofvascular bundles: rachis branches) was higher inannuals (mean = 1.71) than among perennials (mean =1.46). Accessions of annual habit, and adaptedto a wide range of habitats, varied considerably inboth rachis branch (mean = 9.5) and vascular bundlenumbers (mean = 14.0), with V/R ratios similar tothose of perennial growth habit (mean = 1.49).Corresponding measures for both indica and japonica of cultivated rice (O. sativa) variednarrowly and were substantially greater for bothrachis branches (mean = 11.6 and 13.8, respectively)and vascular bundles (mean = 19.1 and 14.8,respectively), with V/R ratios of 1.67 for indica and similar to accessions of O.rufipogon of annual habit, and 1.07 for japonica and lower than accessions of O.rufipogon of both perennial and intermediate habit.Accessions of O. rufipogon from the India andIndochina regions were significantly lower in rachisbranch, but not vascular bundle numbers thanaccessions from China; with the V/R ratio higher amongaccessions from India than found in other geographicregions of origin. The possible role of O.rufipogon accessions of intermediate growth habit inthe evolution of cultivated rice is discussed,although it is speculated that accessions ofintermediate habit with high numbers of rachisbranches and vascular bundles may have resulted frominterspecific hybridization with O. sativacultivars.     

Evaluation of genetic variation among wild rice populations in Cambodia

A total of 448 samples in five natural populations of wild rice (Oryza rufipogon) were collected in Cambodia. They were examined using 12 SSR and two chloroplast markers to evaluate the degree of variation among populations and the genetic structure within populations. In the two annual populations, the number of plants with homozygous alleles at all 12 SSR loci were high (66.3% and 79.5%), suggesting that these plants propagate mainly through self-pollination. In the three perennial populations, no individuals had all homozygous genotypes, but redundant genotypes resulted from clonal propagation were observed. Percentages of the redundant genotypes were highly varied (3.6%, 29.2% and 86.0%). This may be due to the different stable levels of environmental conditions. As for chloroplast genome, most of the wild plants showed the same chloroplast types as most Indica-type cultivars have. However, plants with different chloroplast types were maintained, even in the same population. In tropical Asian countries, many wild rice populations were observed under similar ecological conditions examined in this study. Therefore, the present results concerning population structure will be important to further elucidate genetic features of wild rice, and will also give strong clues to utilize and conserve wild natural genetic resources.     

Allozyme variation and conservation genetics of common wild rice (Oryza rufipogon Griff.) in Yunnan, China

In order to reveal levels and distribution of genetic variation within Oryza rufipogon Griff. of Yunnan, China, where one of the centers of genetic diversity for Asian cultivated rice O. sativa L. is located, allozyme variation encoded by 22 loci was electrophoretically analyzed in 149 individuals of all three existing populations as well as five from other regions (Guangxi, Hainan and Jiangxi provinces) of China. As compared to the level of genetic diversity (the mean A = 1.2, P = 24.1%, Ho = 0.045 and He = 0.079) for the populations from other regions, a rather low genetic diversity (the mean A = 1.1, P = 7.6%, Ho = 0.007 and He = 0.011) was found in Yunnan, which may originate from marginal nature of these populations, recent reduction of populations and consequent drift. The result suggests that the current center of genetic diversity for O. rufipogon fail to agree with that for cultivated rice in China. The genetic differentiation for all the eight populations(F_ST = 0.254) was slightly lower than that for three populations from Yunnan (F_ST = 0.302), indicating a fairly high genetic differentiation in the region. Finally, a conservation plan for sampling/preserving fewer populations but more individuals from each population for the species was given, and an appropriate strategy for conserving the three surviving populations from Yunnan was proposed. This revised version was published online in August 2006 with corrections to the Cover Date.     

Development and evaluation of chromosome segment substitution lines (CSSLs) carrying chromosome segments derived from Oryza rufipogon in the genetic background of Oryza sativa L.

The wild relatives of rice (Oryza sativa L.) are useful sources of alleles that have evolved to adapt in diverse environments around the world. Oryza rufipogon, the known progenitor of the cultivated rice, harbors genes that have been lost in cultivated varieties through domestication or evolution. This makes O. rufipogon an ideal source of value-added traits that can be utilized to improve the existing rice cultivars. To explore the potential of the rice progenitor as a genetic resource for improving O. sativa, 33 chromosome segment substitution lines (CSSLs) of O. rufipogon (W0106) in the background of the elite japonica cultivar Koshihikari were developed and evaluated for several agronomic traits. Over 90% of the entire genome was introgressed from the donor parent into the CSSLs. A total of 99 putative QTLs were detected, of which 15 were identified as major effective QTLs that have significantly large effects on the traits examined. Among the 15 major effective QTLs, a QTL on chromosome 10 showed a remarkable positive effect on the number of grains per panicle. Comparison of the putative QTLs identified in this study and previous studies indicated a wide genetic diversity between O. rufipogon accessions.     

控制普通野生稻种子休眠性QTL的定位

水稻种子休眠性是关系到稻米品质和稻种质量的一个重要农艺性状。研究水稻种子休眠性遗传及分子机制对培育具有适度休眠性的优良水稻品种具有重要意义。本研究以籼稻品种9311为受体、普通野生稻为供体的染色体片段置换系群体为材料,在后熟不同时间检测群体种子休眠性,对控制种子休眠性的QTL进行定位分析,共定位到14个QTL,分布在第3、第4、第5、第6、第7、第10、第11、第12染色体上。筛选休眠性显著强于背景亲本9311的家系,分析这些家系携带的QTL数目,表明携带的位点越多,休眠性越强。进一步利用家系Q14与9311的F2群体验证了第7染色体标记RM180和RM21323之间存在一个效应较大的QTL qSD-7-2,该位点LOD值为18.49,可解释的表型变异率为33.53%,表明该位点是一个控制普通野生稻种子休眠性的主效QTL,且能稳定遗传。本研究为野生稻种子休眠基因的精细定位及克隆奠定了基础,且为培育强休眠性籼稻品种提供了育种材料。     

Quantitative trait loci for whiteness of cooked rice detected in improved rice cultivars in Hokkaido

Improving the eating quality of cooked rice has been one of the most important objectives in rice breeding programs. Eating quality of cooked rice is a complex trait including several components, such as external appearance, taste, aroma, and texture. Therefore, dissection of these components followed by marker-assisted selection of detected QTL(s) may be a useful approach for achieving desirable eating quality in rice breeding. Whiteness of cooked rice (WCR) is an important factor related to the external appearance of cooked rice. WCR is known to be associated with the amylose and protein contents of the endosperm. However, the genetic basis of WCR remains unclear. In this study, we evaluated phenotypic variation in WCR among recently developed rice cultivars from Hokkaido, Japan. Then, we developed doubled haploid lines (DHLs) derived from a cross between two cultivars from Hokkaido, Joiku No. 462 (high WCR) and Jokei06214 (low WCR). Using the DHLs, we detected two QTLs for WCR, qWCR3 and qWCR11, on chromosomes 3 and 11, respectively. We also examined the dosage effect of the two QTLs based on both the categorized segregants in the DHLs and the relationship between the WCR phenotype and inheritance around the QTL regions in cultivars from Hokkaido.     

Mapping quantitative trait loci influencing panicle‐related traits from Chinese common wild rice (Oryza rufipogon) using introgression lines

Panicle‐related traits are important agronomic traits which directly associated with grain yield. In this study, we investigated quantitative trait loci (QTLs) associated with panicle‐related traits using a set of 265 introgression lines (ILs) of common wild rice (Oryza rufipogon Griff.) in the background of Indica high‐yielding cultivar Guichao 2 (O. sativa L.). A total of 39 QTLs associated with panicle‐related traits including panicle length (PL), primary branch number (PBN), secondary branch number (SBN), spikelet number per panicle (SPP) and spikelet density (SD), were detected in the ILs with single‐point analysis. The alleles of 20 QTLs derived from wild rice showed positive effects, and some QTLs, such as, QPl1b for PL, QPbn8 for PBN, QSd4 and QSd11b for SD and QSpp4 for SPP showed larger positive effects, providing good candidates and useful information for marker‐aided improvement of yield potential of rice. Most of the QTLs controlling SPP, SBN and SD were located in cluster or closely linked on chromosomes, and the directions of their additive effects were consistent, which explained the genetic basis of significant correlations between their phenotypic characters.     

Variation in heading date conceals quantitative trait loci for other traits of importance in breeding selection of rice

To identify quantitative trait loci (QTLs) associated with the primary target traits for selection in practical rice breeding programs, backcross inbred lines (BILs) derived from crosses between temperate japonica rice cultivars Nipponbare and Koshihikari were evaluated for 50 agronomic traits at six experimental fields located throughout Japan. Thirty-three of the 50 traits were significantly correlated with heading date. Using a linkage map including 647 single-nucleotide polymorphisms (SNPs), a total of 122 QTLs for 38 traits were mapped on all rice chromosomes except chromosomes 5 and 9. Fifty-eight of the 122 QTLs were detected near the heading date QTLs Hd16 and Hd17 and the remaining 64 QTLs were found in other chromosome regions. QTL analysis of 51 BILs having homozygous for the Koshihikari chromosome segments around Hd16 and Hd17 allowed us to detect 40 QTLs associated with 27 traits; 23 of these QTLs had not been detected in the original analysis. Among the 97 QTLs for the 30 traits measured in multiple environments, the genotype-by-environment interaction was significant for 44 QTLs and not significant for 53 QTLs. These results led us to propose a new selection strategy to improve agronomic performance in temperate japonica rice cultivars.     

Identification of qRL7, a major quantitative trait locus associated with rice root length in hydroponic conditions

Root system development is an important target for improving yield in rice. Active roots that can take up nutrients more efficiently are essential for improving grain yield. In this study, we performed quantitative trait locus (QTL) analyses using 215 recombinant inbred lines derived from a cross between Xieqingzao B (XB), a maintainer line with short roots and R9308, a restorer line with long roots. Only a QTLs associated with root length were mapped on chromosomes 7. The QTL, named qRL7, was located between markers RM3859 and RM214 on chromosome 7 and explained 18.14–18.36% of the total phenotypic variance evaluated across two years. Fine mapping of qRL7 using eight BC₃F₃ recombinant lines mapped the QTL to between markers InDel11 and InDel17, which delimit a 657.35 kb interval in the reference cultivar Nipponbare. To determine the genotype classes for the target QTL in these BC₃F₃ recombinants, the root lengths of their BC₃F₄ progeny were investigated, and the result showed that qRL7 plays a crucial role in root length. The results of this study will increase our understanding of the genetic factors controlling root architecture, which will help rice breeders to breed varieties with deep, strong and vigorous root systems.     

Mapping of quantitative trait loci controlling seed longevity of rice (Oryza sativa L.) after various periods of seed storage

Seed longevity varies considerably in cultivated rice (Oryza sativa L.), but the underlying genetic mechanism of longevity has not been well elucidated. Quantitative trait loci (QTL) that control seed longevity after various periods of seed storage were sought using recombinant inbred lines derived from a combination involving ‘Milyang23’(Indica‐type) and ‘Akihikari’ (Japonica‐type). In all, 12 QTLs for germination and normal seedling growth were detected as indices of seed longevity on chromosome 7 (one region) and chromosome 9 (two regions) in treated seeds that had been stored under laboratory conditions for 1, 2 or 3 years.‘Milyang23’ alleles of all QTLs promoted germination and normal seedling growth after all durations of storage. These QTL regions were detected repeatedly in more than one seed condition. Therefore, we infer that these regions control seed longevity.     

A source of resistance to seed shattering in kleingrass,Panicum coloratum L.

Summary Seed of kleingrass, P. coloratum, ripen nonuniformly and shatter readily at maturity. Consequently, it is difficult to maximize both seed quality and yield. A source of resistance to seed shattering is needed. In this investigation, two kleingrass populations, the cultivar Selection-75, and an introduction from South Africa, PI 410177, were evaluated for seed shattering during three seed production seasons. Individual inflorescences from field-grown plants were enclosed in seed traps and all shattered seed was collected at weekly intervals until 49 days after anthesis. Although there were seasonal differences, PI 410177 always shattered seed at a slower rate than Selection-75 in each of the three seasons. Averaged over all seasons Selection-75 had shattered 74% of its seed by 49 days after anthesis while PI 410177 shattered only 37%. A separate greenhouse-field experiment demonstrated that seasonal differences in seed shattering are primarily the result of varying weather conditions during the period of seed production. PI 410177 is the first reported source of resistance to seed shattering in P. coloratum.     

利用东乡普通野生稻染色体片段置换系定位产量相关性状QTL

以东乡普通野生稻和日本晴为亲本构建的染色体片段置换系为研究材料, 2019年分别在北京、山东临沂和江西南昌对分蘖数、穗粒数和粒形等11个产量相关性状进行多环境鉴定,结合染色体片段置换系基因型数据定位水稻产量相关性状QTL。3个环境共检测到68个QTL,包括株高4个、穗长5个、分蘖数2个、一次枝梗数7个、一次枝梗粒数8个、二次枝梗数8个、二次枝梗粒数10个、每穗粒数6个、千粒重7个、粒长8个和粒宽3个; LOD值介于2.50～12.66之间,贡献率变幅为4.67%～27.79%,15个QTL的贡献率大于15%;24个QTL与已报道位点/基因位置重叠,44个QTL为新发现位点; 6个QTL在2个环境能被检测到, 1个QTL qTGW2能在3个环境检测到,且是还未报道的新位点。最后,利用BSA法验证了qPH7、qPBPP8-2和qGW10三个QTL的可靠性。本研究将为后续产量相关性状基因克隆以及进一步解析其遗传基础和分子调控机制奠定基础。     

Mapping of quantitative trait loci for phytic acid and phosphorus contents in seed and seedling of mungbean (Vigna radiata (L.) Wilczek)

Phytic acid (PA) is the storage form of phosphorus (P) in seeds and plays an important role in the nutritional quality of food crops. There is little information on the genetics of seed and seedling PA in mungbean [Vigna radiata (L.) Wilczek]. Quantitative trait loci (QTL) were identified for phytic acid P (PAP), total P (TP), and inorganic P (IP) in mungbean seeds and seedlings, and for flowering, maturity and seed weight, in an F₂ population developed from a cross between low PAP cultivated mungbean (V1725BG) and high PAP wild mungbean (AusTRCF321925). Seven QTLs were detected for P compounds in seed; two for PAP, four for IP and one for TP. Six QTLs were identified for P compounds in seedling; three for PAP, two for TP and one for IP. Only one QTL co-localized between P compounds in seed and seedling suggesting that low PAP seed and low PAP seedling must be selected for at different QTLs. Seed PAP and TP were positively correlated with days to flowering and maturity, indicating the importance of plant phenology to seed P content.     

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.     

Confirming a major QTL and finding additional loci responsible for field resistance to brown spot (Bipolaris oryzae) in rice

Brown spot is a devastating rice disease. Quantitative resistance has been observed in local varieties (e.g., ‘Tadukan’), but no economically useful resistant variety has been bred. Using quantitative trait locus (QTL) analysis of recombinant inbred lines (RILs) from ‘Tadukan’ (resistant) × ‘Hinohikari’ (susceptible), we previously found three QTLs (qBS2, qBS9, and qBS11) that conferred resistance in seedlings in a greenhouse. To confirm their effect, the parents and later generations of RILs were transplanted into paddy fields where brown spot severely occurred. Three new resistance QTLs (qBSfR1, qBSfR4, and qBSfR11) were detected on chromosomes 1, 4, and 11, respectively. The ‘Tadukan’ alleles at qBSfR1 and qBSfR11 and the ‘Hinohikari’ allele at qBSfR4 increased resistance. The major QTL qBSfR11 coincided with qBS11 from the previous study, whereas qBSfR1 and qBSfR4 were new but neither qBS2 nor qBS9 were detected. To verify the qBSfR1 and qBSfR11 ‘Tadukan’ resistance alleles, near-isogenic lines (NILs) with one or both QTLs in a susceptible background (‘Koshihikari’) were evaluated under field conditions. NILs with qBSfR11 acquired significant field resistance; those with qBSfR1 did not. This confirms the effectiveness of qBSfR11. Genetic markers flanking qBSfR11 will be powerful tools for marker-assisted selection to improve brown spot resistance.     

Two linked genes on rice chromosome 2 for F1 pollen sterility in a hybrid between Oryza sativa and O. glumaepatula

Hybrid incompatibility plays an important role in establishment of post-zygotic reproductive isolation. To unveil genetic basis of hybrid incompatibilities between diverged species of genus Oryza AA genome species, we conducted genetic dissection of hybrid sterility loci, S22(t), which had been identified in backcross progeny derived from Oryza sativa ssp. japonica (recurrent parent) and South American wild rice O. glumaepatula near the end of the short arm of chromosome 2. The S22(t) region was found to be composed of two loci, designated S22A and S22B, that independently induce F₁ pollen sterility. Pollen grains containing either of the sterile alleles (S22A-glum^s or S22B-glum^s) were sterile if produced on a heterozygous plant. No transmission of the S22A-glum^s allele via pollen was observed, whereas a low frequency of transmission of S22B-glum^s was observed. Cytological analysis showed that the sterile pollen grains caused by S22A could reach the bicellular or tricellular stage, and the nearly-sterile pollen grains caused by S22B could reach the tricellular stage. Our genetic analysis showed repulsion linkage effect is possible to induce strong reproductive barrier by high pollen sterility based on recombination value and transmission ratio of hybrid sterility gene to the progeny was influenced by frequency of competitors on fertilization.     

Identification of quantitative trait loci associated with boiled seed hardness in soybean

Boiled seed hardness is an important factor in the processing of soybean food products such as nimame and natto. Little information is available on the genetic basis for boiled seed hardness, despite the wide variation in this trait. DNA markers linked to the gene controlling this trait should be useful in soybean breeding programs because of the difficulty of its evaluation. In this report, quantitative trait locus (QTL) analysis was performed to reveal the genetic factors associated with boiled seed hardness using a recombinant inbred line population developed from a cross between two Japanese cultivars, ‘Natto-shoryu’ and ‘Hyoukei-kuro 3’, which differ largely in boiled seed hardness, which in ‘Natto-shoryu’ is about twice that of ‘Hyoukei-kuro 3’. Two significantly stable QTLs, qHbs3-1 and qHbs6-1, were identified on chromosomes 3 and 6, for which the ‘Hyoukei-kuro 3’ alleles contribute to decrease boiled seed hardness for both QTLs. qHbs3-1 also showed significant effects in progeny of a residual heterozygous line and in a different segregating population. Given its substantial effect on boiled seed hardness, SSR markers closely linked to qHbs3-1, such as BARCSOYSSR_03_0165 and BARCSOYSSR_03_0185, could be useful for marker-assisted selection in soybean breeding.