Detection and validation of QTLs associated with seed longevity in rice (Oryza sativa L.)

Seed longevity in rice is a major determinant in seed production and germplasm preservation. In this paper, a recombinant inbred line (RIL) population consisting of 172 lines derived from the cross between Xiang743 and ‘Katy’ was used to map quantitative trait loci (QTLs) for seed longevity (SL) after seed storage for 18 and 30 months under ambient conditions. Two putative QTLs, qSL‐2 and qSL‐8, were detected and located on chromosomes 2 and 8, respectively. qSL‐2 is an allele from Xiang743 allele and increases seed longevity. qSL‐8 was a novel QTL from ‘Katy’ allele and increases seed longevity. qSL‐8 explained 15.29% and 17.35% of the phenotypic variance after seed storage for 18 and 30 months, respectively. Furthermore, qSL‐8 was validated in a secondary population developed by self‐pollination of a residual heterozygous line (RHL) selected from the RIL population, which explained 25.93% of the phenotypic contribution. These results provide an opportunity for map‐based cloning of qSL‐8. Furthermore, qSL‐8 may be a target for improving seed longevity by marker‐assisted selection (MAS) in rice.     

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。     

Detection of QTLs for white-back and basal-white grains caused by high temperature during ripening period in japonica rice

There is increasing evidence that global warming affects the development of rice. High temperatures during ripening increase the ratio of undesirable chalky grains followed by deteriorating grain appearance quality. In order to detect quantitative trait loci (QTLs) controlling the occurrence of white-back and basal-white chalky grains of brown rice, QTL analysis was performed using recombinant inbred lines derived from a cross between two strains, ‘Tsukushiroman’ (sensitive to heat stress) and ‘Chikushi 52’ (tolerant of heat stress). The F₇ and F₈ lines were exposed to heat stress during the ripening period in two locations, Fukuoka and Kagoshima, in Japan. QTLs for white-back grains and basal-white grains were detected on chromosomes 1, 3, and 8, and those for basal-white grains were detected on chromosomes 2, 3, and 12. QTLs on chromosome 8 for white-back grains were shared in the plants grown in both locations. Near-isogenic lines (NILs), which harbored a segment from ‘Chikushi 52’ on chromosome 8 with the genetic background of ‘Tsukushiroman’, showed relatively lower ratios of white-back grains than ‘Tsukushiroman’. Therefore, insertion of the ‘Chikushi 52’ genomic region of the QTL on chromosome 8 can improve the quality of rice when it is grown under heat stress conditions.     

控制水稻RIL群体化感作用的QTL定位研究

此研究以“莱蒙”（弱化感）和“多拉”（强化感）水稻杂交产生的重组自交系（recombinant inbred lines,RILs）及其亲本为供体植物,并以稻田主要杂草稗草为受体植物,采用迟播共培法测定与各家系及亲本共培稗草的根长,并转化成抑制率来表征化感作用。结果表明群体及亲本根长抑制率基本呈正态分布,且用它来表征化感作用是适合的。运用分子标记技术构建了该群体的遗传图谱,共97个分子标记,覆盖水稻12条连锁群。QTL定位检测到控制水稻化感作用的5个QTL,分别位于1、1、5、9、9号连锁群,解释了23.97%、15.21%、13.89%、18.63%、6.64%的遗传变异。进一步证实水稻化感作用存在主效QTL,同时为分子育种提供依据。     

Detection and analysis of QTLs for ferrous iron toxicity tolerance in rice, Oryza sativa L.

A mapping population of 96 BC₁F₉lines (Backcross Inbred Lines: BILs),derived by a single-seed descent method rom a backcross of Nipponbare (japonica) / Kasalath (indica // Nippon are, was used to detect quantitative trait loci (QTLs) for leaf bronzing index (LBI), stem dry weight (SDW), tiller number (TN) and root dry weight (RDW) under Fe²⁺ stress condition in rice. Two parents and 96 BILs were phenotyped for the traits by growing them in Fe²⁺ toxicity nutrient solution. A total of four QTLs were detected on chromosome 1 and 3, respectively, with LOD of QTLs ranging from 3.17 to 7.03. One QTL controlling LBI, DW, N and RDW was located at the region of C955-C885 on chromosome 1, and their contributions to whole variation were 20.5%, 36.9%, 43.9% and 38.8%,respectively. The QTL located at the region of C955-C885 on chromosome 1 may be important to ferrous iron toxicity tolerance in rice. Another QTL for SDW and RDW was located at the region of C25-C515 on chromosome 3, with respective contributions of 47.9% and 35.0% to whole variation. Further, two QTLs on chromosome 1 were located for RDW at the region of R2329-R210 and for TN at the region of R1928-C178. Comparing with the other mapping results, the QTL located at the region of C955-C885 on chromosome 1 was identical with the results reported previously. There is a linkage between a TL detected under Fe²⁺ stress condition for stem and root dry weight and a QTL detected under phosphorus-deficiency condition for dry weight on chromosome 3. This revised version was published online in July 2006 with corrections to the Cover Date.     

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.     

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.     

Bulked segregant analysis to detect main effect QTL associated with grain quality parameters in Basmati 370/ASD 16 cross in rice Oryza sativa L) using SSR markers

In the present study a population consisting of 247 F₂ individuals from the cross between Basmati 370, a superior quality basmati variety and ASD16, a non-basmati high-yielding variety was analyzed for their segregation pattern of grain length (GL), grain breadth (GB), cooked grain length (CGL), cooked grain breadth (CGB), and gelatinization temperature (GT). Except GT, all other traits showed normal distribution indicating the polygenic control over the traits. The correlation analysis between traits indicated that GT had positive significant association with GL (0.125), and CGL (0.243). To identify main effect QTL (MQTL) for the above grain quality traits, both the parents were surveyed with 86 primer pairs of simple sequence repeats (SSR). The parental survey revealed 63.95% polymorphism between parents. In order to detect the MQTL associated with grain quality traits, a strategy of combining the DNA pooling from selected segregants and genotyping was adopted. The number of individuals forming the bulk influenced the identification of putative marker(s) for each of the traits. The association of putative markers identified based on DNA pooling from selected segregants was established by Single Marker Analysis (SMA). The results of SMA revealed that SSR markers, RM225 on chromosome #6 and RM247 on chromosome #12 showed significant association with GB and CGB respectively. It is established that molecular marker analysis involving DNA pooling of phenotypic extremes and selective genotyping helps to detect MQTL for complex traits involving early segregating generations. The molecular marker analysis involving the DNA pooling of phenotypic extremes could be a useful strategy to detect the genetic loci with major effects of other complex grain quality traits in rice.     

Developmental changes of phyllochron in near-isogenic lines of rice (Oryza sativa L.) with different growth durations

The repeated elements called phytomers, which consist of leaf, node, internode and axillary bud, play an important role in the development of modular organization in plants. Rice has the striking feature that the rate of the phytomer production is closely synchronized with the rate of leaf emergence (phyllochron). We examined developmental changes of phyllochron by using 10 near-isogenic lines (NILs) showing diversified growth durations in rice. The NILs were established by backcrosses with a strain practically insensitive to photoperiod, and they consisted of early- or late-flowering NILs whose differences of growth duration were caused by the combinations of alleles at 6 loci. The developmental patterns of phyllochron were evaluated by means of a quartic polynomial, which fitted well in most cases. The results indicated that phyllochron greatly changed during development, especially in late-flowering NILs as well as the recurrent parents, although the fluctuation of phyllochron was not so marked in the early-flowering NILs. Thus, the developmental change of phyllochron was highly dependent upon the genotypes and/or growth duration; however, it was associated with neither floral initiation nor temperature, indicating that the change of phyllochron might reflect internal or physiological changes which occur during the life cycle of rice. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic progress of upland rice (Oryza sativa L.) lines for disease resistance

The rice crop is affected by diseases throughout its cycle, impacting negatively on grain yield and quality. The control of the disease impact can be accomplished via crop breeding, using highly multiple resistant genotypes. This study aimed to evaluate the efficiency of multiple-character and specific selection of multiple resistance to major culture-associated diseases (neck blast, leaf scald and grain discoloration) in rice lines of the Upland Rice Genetic Breeding Program. The experiments were conducted in 35 sites during 12 agricultural years, where 124 lines were evaluated for the severity of fungal diseases, under natural field conditions. Multiple parameters were calculated based on the diseases´ scores: genetic, phenotypic and environmental variances, heritability, selection gain, renewal rate, and genetic and renewal progress. Genetic variance for the disease resistance was identified in the population, and the selection gain for multiple-character selection was of 3.16 year⁻¹ throughout the breeding process with a renewal rate of over 35%. The programme has showed efficiency in selecting multiple resistant genotypes to the mentioned diseases, highlighting genotypes with high potential for market release.     

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.     

Tagging quantitative trait loci associated with grain yield and root morphological traits in rice (Oryza sativa L.) under contrasting moisture regimes

Plant breeding for drought-prone habitats envisages a favorable combination of grain yield and drought resistance. Though several components enhancing drought resistance have been identified in rice,their association with grain yield, under low-moisture stress, has been established in very few instances. We attempt to study the associations between rice grain yield and root system parameters both at phenotypic and genotypic levels. The doubled haploid population of IR64/Azucena was evaluated for root related traits at peak vegetative stage and grain yield related traits under both low-moisture stress and non stress conditions. ‘Mean environment’ was computed for yield related traits. Correlation and QTL mapping was attempted to find out the associations. The correlation between maximum root length and grain yield was positive under stress and negative in non stress. Genotypes with thicker and deeper roots, manifested higher biomass and grain yield under stress. Only one QTL found to increase days to flowering in non stress was also found to influence root volume and dry weight negatively under stress. The study suggests that loci enhancing grain yield and related traits were not pleiotropic with loci for desirable root morphological traits studied under low-moisture stress at vegetative stage, in the genetic material used in the study. It is thus possible to combine higher grain yield and desirable root morphological traits, favorably, to enhance productivity of rice under low-moisture stress. In rainfed ecologies, where deep roots contribute to enhanced drought resistance in rice, the results indicate the possibility of combining drought resistance with higher levels of grain yield. This revised version was published online in August 2006 with corrections to the Cover Date.     

稻米直链淀粉含量基因座位的分子标记定位

以直链淀粉含量(AC)中等的CT9993和泰国优质的香软米KDML105杂交产生的152个重组近交系 (RIL)为材料, 构建了含83个RFLP、 69个AFLP和15个微卫星(SSLP)标记的分子标记连锁图 , 标记间平均距离为12.98 cM。 应用该连锁图对控制稻米AC的基因座位(QTL)进行了分析 。 结果表明： 稻米AC主要受两个主效QTL和5个微效QTL的共同控制     

Genomic regions associated with milling quality and grain shape identified in a set of random introgression lines of rice (Oryza sativa L.)

Rice milling quality is the final part of grain yield making it fit for eating and a complex trait that remains poorly understood genetically. Three components of rice milling quality, i.e. brown rice rate, milled rice rate and head rice rate and related rice grain shape traits were genetically dissected by the QTL mapping approach using a set of 231 random rice introgression lines and 160 SSR markers. A total of 10 genomic regions were found to be associated with rice grain shape and milling quality traits. Of these, one major QTL on chromosome 7 had large effects on rice grain shape and milling quality and was detected consistently in several related populations of rice, which offers an opportunity for marker‐aided improvement of rice milling quality and QTL cloning.     

粳稻杂种优势遗传基础剖析

为了解控制粳稻产量相关性状及其中亲优势的基因作用类型, 利用秀堡RIL群体及其2个回交(BCF₁)群体对株高、生育期、单株有效穗数、穗长、每穗颖花数、结实率、一次枝梗数和二次枝梗数8个性状及其中亲杂种优势进行QTL定位。共检测到58个显著的主效QTL (M-QTL), 单个M-QTL的贡献率变幅为3.3%~41.9%。77.6%的M-QTL表现为加性效应, 15.5%的M-QTL表现为部分或完全显性效应, 6.9%的M-QTL表现为超显性效应。共检测到90对显著的双基因上位性QTL(E-QTL)。在RIL群体中检测到44对E-QTL, 单对E-QTL的贡献率变幅为1.7%~8.0%, 平均3.7%。在XSBCF₁群体中检测到27对E-QTL, 其中利用BCF₁表型值检测到16对E-QTL, 单对E-QTL的贡献率变幅为12.7%~78.5%, 平均29.2%; 利用中亲优势值检测到11对E-QTL, 单对E-QTL的贡献率变幅为15.0%~71.8%, 平均40.1%。在CBBCF₁群体中检测到19对E-QTL, 其中利用BCF₁表型值检测到12对E-QTL, 单对E-QTL的贡献率变幅为2.7%~64.4%, 平均30.1%; 利用中亲优势值检测到9对E-QTL, 单对E-QTL的贡献率变幅为21.7%~64.1%, 平均40.0%。在CBBCF₁群体中, 利用BCF₁表型值和中亲优势值都检测到的E-QTL有2对。上述结果表明上位性效应是粳稻秀堡组合杂种优势的主要遗传基础。     

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.