Mapping QTLs related to salinity tolerance of rice at the young seedling stage

Using a population of recombinant inbred lines of the 164 genotypes derived from a cross between ‘Milyang 23’ (indica) and ‘Gihobyeo’ (japonica) in rice (Oryza sativa L.), salt tolerance was evaluated at a young seedling stage in concentrations of 0.5% and 0.7% NaCl. Mapping quantitative trait loci (QTLs) related to salt tolerance was carried out by interval mapping using Qgene 3.0. Two QTLs (qST1 and qST3) conferring salt tolerance at young seedling stage were mapped on chromosome 1 and 3, respectively, and explained 35.5–36.9% of the total phenotypic variation in 0.5% and 0.7% NaCl. The favourable allele of qST1 was contributed by ‘Gihobyeo’, and that of qST3 by ‘Milyang 23’. The results obtained in 0.5% and 0.7% NaCl for 2 years were similar in flanked markers and phenotypic variation.     

A major QTL associated with cold tolerance at seedling stage in rice (Oryza sativa L.)

Chilling injury is one of the most important limiting factors affecting rice production in temperate and high-elevation areas. In this study, 146 microsatellite markers were employed to identify quantitative trait loci (QTL) conferring cold tolerance at seedling stage (CTS) .The mapping population consisted of 193 doubled haploid (DH) lines, which derived from a cross between a cold-tolerant japonica variety (AAV002863) and a cold-sensitive indica cultivar (Zhenshan97B). Tolerance to cold was assessed by the survival percentage of seedlings after cold treatment. In a climate chamber, after treatment at 6°C/10°C for 7 d, the measurement was taken on the sixth day of the recovery stage at room temperature. The phenotypic distribution of the DH population approximately fitted normality with skewness and kurtosis less than 0.3, and the difference among the three repetitions was not significant. Five main effect QTLs were identified with LOD > 4.0 on chromosomes 1, 2, 8 using a composite interval mapping approach. The accumulated contribution of the five QTLs was 62.28%, and a major QTL (LOD = 15.09) was identified on chromosome 2 flanked by RM561 and RM341, which explained 27.42% of the total phenotypic variation. Four significant epistatic interactions were also detected with a total contribution of 20.14%. Liang Chen and Qiaojun Lou had made the equal contribution for the research.     

Genetic analysis of salt tolerance at seedling and reproductive stages in rice (Oryza sativa)

Salinity is a major abiotic stress that limits rice production across rice areas as high‐yielding modern rice varieties are generally sensitive to salt stress. The study was conducted to deduce heritability and combining ability estimates of rice for various morphological and physiological traits using a 7 × 7 full‐diallel‐cross analysis at seedling and reproductive stages. The salinity stress treatment was 12 dS m^?1 at the seedling stage and 8 dS m^?1 at the reproductive stage. Diallel analysis revealed high for salinity tolerance scores and shoot height, moderate for shoot dry weight and root dry weight and low for Na⁺ and K⁺ concentrations and K⁺/Na⁺ ratio. The low‐to‐moderate narrow‐sense heritability for number of panicles, number of fertile spikelets, grain weight, spikelet fertility and K⁺/Na⁺ ratio suggests a large breeding population and delayed selection for tolerance until later generations. Significant maternal effects indicate that selection of the female parent is very important for desired trait development. The results of this study confirmed that salinity tolerance at the seedling and reproductive stages is regulated by a different set of genes that could be pyramided using different donors to enhance the level of tolerance.     

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.     

QTL analysis for soil‐surface roots originating from a New Plant Type rice (Oryza sativa L.)

The introgression line YTH16 harbouring chromosome segments from the New Plant Type cultivar IR65600–87–2‐2–3 with genetic background of an Indica Group rice IR 64 forms soil‐surface roots. To clarify the genetic mechanism, QTL analysis was performed using hybrid populations derived from a cross between IR 64 and YTH16. A total of eight QTLs were detected in the three introgressed segments on chromosomes 2, 5 and 7. Seven chromosome segment lines (CSLs) combining these three QTL regions were selected from the progenies. The two CSLs harbouring a single region (excluding the CSL with a region on chromosome 5) showed high scores and low means of root angle distribution in comparison with IR 64. Four CSLs harbouring two or three regions showed high scores and low means of root angle distribution in comparison with YTH16 and the CSLs harbouring a single QTL region. These results indicated that the soil‐surface rooting of YTH16 was controlled by the three QTLs’ regions and that chr. 5 particularly played a role in supporting the effect with others.     

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.     

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。     

QTL mapping for seedling traits associated with low‐nitrogen tolerance using a set of advanced backcross introgression lines of rice

Nitrogen (N) deficiency is a major yield‐limiting factor in rice production. The objective of this study was to identify putative QTLs for low‐N stress tolerance of rice, using an advanced backcross population derived from crosses between an indica cultivar ‘93‐11’ and a japonica cultivar ‘Nipponbare’ and genotyped at 250 marker loci. Plant height, maximum root length, root dry weight, shoot dry weight and plant dry weight under two N conditions and their relative traits were used to evaluate low‐N tolerance at the seedling stage. A total of 44 QTLs were identified on chromosomes 1, 2, 3, 4, 5, 6, 8 and 9. Eight intervals on five chromosomes were identified to harbour multiple QTLs, suggesting pleiotropism or multigenic effects according to the contributor of alleles. Some QTL clusters were found in the nearby regions of genes associated with N recycling in rice, indicating that the key N metabolism genes might have effects on the expression of QTLs. Several unique QTLs for relative traits were detected, which suggested the specific genetic basis of relative performance.     

水稻苗期耐Cd胁迫的QTL定位分析

[目的]进行水稻苗期耐Cd胁迫的QTL初步定位。[方法]（1）以Lemont（美国）和Dular（印度）杂交建立的重组自交系（RILs）群体,包括123个家系和亲本在内,用含有0.2mg/L镉的水培液进行处理,以不加镉培养的水培液作为对照,考察了叶绿素含量、根长、株高、叶长等4个性状,并转换成抗性指数,用于评价水稻对Cd污染的抗性指标。（2）在已构建的以109个引物为基础的遗传图谱上进行复合区间定位。[结果]（1）共检测到9个加性QTLs,涉及1,2,3,11等4条染色体,其中,以叶绿素抗性指数为指标,检测到3个与耐Cd有关的QTLs 分别位于第2,3,11染色体上,解释了14%,9%,9%的表型变异;（2）以根长抗性指数为评价指标,只定到1个位于第1染色体上控制耐Cd的QTLs,解释了9%的表型变异; （3）用株高抗性指数进行定位,共有3个与耐Cd相关的QTLs,位于1,1,11染色体上,分别解释了10%,27%,10%的表型变异;（4）而以叶长抗性指数进行水稻秧苗耐Cd性表现的QTL定位,结果发现也有2个QTLs与其耐Cd 反应有关,它们分别位于1,11染色体上,解释了21%,12%的表型变异。分析表明,在采用不同评价指标所检测到的9个与耐Cd相关的QTLs中,有7个集中于第1和第11染色体上,其中第1染色体上有4个,第11染色体上有3个。（结论）以株高和叶绿素抗性指数为评价指标,检测到的QTLs最多,根长抗性指数为评价指标的最少。研究还发现在第1和第11染色体上的相同区间内同时检测到以不同抗性指数为评价指标的多个与耐Cd相关的QTLs,推测它们可能是功能相同的几个紧密连锁的非等位基因,也可能就是同一等位基因的不同表现形式,从而也说明了该评价指标用于基因定位的准确性和可行性。     

Mapping of quantitative trait loci associated with rice black‐streaked dwarf virus disease and its insect vector in rice (Oryza sativa L.)

Rice black‐streaked dwarf virus disease (RBSDVD), transmitted by small brown planthopper (SBPH, Laodelphax striatellus), causes serious loss in rice production. Breeding resistant cultivars are one of the most effective strategies to control the virus disease and its vector. By both natural inoculations in the field and modified seedling‐box screening test in the glasshouse, an indica variety WR24 showed high resistance to RBSDVD and SBPH. An F_2:3 population consisting of 153 lines derived from a cross between WR24 and a susceptible japonica variety Suyunuo was used for quantitative trait loci (QTL) analysis of RBSDVD and SBPH resistance. The linkage map consisting of 130 SSR markers was constructed with an average marker interval of 13.90 cM, spanning a total of 1890.9 cM. Totally, five QTLs for RBSDV resistance, viz. qRBSDV3^WR24, qRBSDV6^WR24, qRBSDV7^WR24, qRBSDV9^WR24 and qRBSDV11^WR24, were detected on chromosomes 3, 6, 7, 9 and 11, with LOD scores of 2.7, 3.08, 3.13, 5.28 and 3.7, respectively. Meanwhile, three QTLs for SBPH resistance, including qSBPH5^WR24, qSBPH7^WR24 and qSBPH10^WR24, were mapped on chromosomes 5, 7 and 10, with LOD scores of 2.18, 3.5 and 3.57, respectively. All resistant alleles were from WR24. Among these QTLs, qRBSDV7^WR24, qSBPH5^WR24 and qSBPH10^WR24 were newly reported, and qSBPH10^WR24 showed major effect that explained 17.9% of total phenotypic variance. The RBSDVD and SBPH resistance QTLs and the tightly linked DNA markers can be utilized in RBSDV and SBPH resistance breeding in rice.     

Identification of QTLs controlling rice drought tolerance at seedling stage in hydroponic culture

‘Drought avoidance’ and ‘drought tolerance’ are two mechanisms by which plants adapt under water stress. These mechanisms are difficult to evaluate separately in field experiments. Using hydroponic culture, we studied the genetic control of drought tolerance in rice (Oryza sativa L.) without the effect of drought avoidance. A backcross inbred population of ‘Akihikari’ (lowland cultivar) × ‘IRAT109’ (upland cultivar) with 106 lines was cultured with (stressed condition) and without (non-stressed condition) polyethylene glycol (PEG) at seedling stage. The relative growth rate (RGR), specific water use (SWU), and water use efficiency (WUE) showed significant genotype × environment interactions with or without PEG, indicating that each line responded differently to water stress. A quantitative trait locus (QTL) analysis revealed that these interactions were QTL specific. A total of three QTLs on chromosomes 2, 4, and 7 were detected for RGR. The QTL on chromosome 7 had a constant effect across environments, while the QTL on chromosome 4 had an effect only under non-stressed condition and that on chromosome 2 only under stressed condition. The stress-specific QTL on chromosome 2 was not co-located with any QTLs for root system depth previously reported from the same mapping population. However, this QTL was co-located with a stress-specific QTL for SWU, suggesting that the control of transpiration was relevant to dry matter production under drought. We concluded that PEG-treated hydroponic culture is very effective for use in genetic analyses of drought tolerance at seedling stage.     

水稻基部伸长节间性状与倒伏相关性分析及QTL定位

利用珍汕97B/密阳46 RILs群体及其构建的连锁图谱，对水稻株高和基部Ⅰ、Ⅱ伸长节间性状与稻株抗倒伏能力进行相关分析，并对基部Ⅰ、Ⅱ伸长节间性状进行QTL定位，共检测到加性效应QTLs 16个、加性´加性互作33对。估算了每个QTL的加性效应值和每对加加互作的上位性效应值，比较了QTLs的基因组分布。在第1染色体短臂和第     

水稻抽穗期基因定位及其环境互作研究

为构建SSR分子标记技术构建其遗传图谱,利用由小穗小粒型品种‘密阳46’和大穗大粒型品种FJCD建立的一个包含130个家系F10的重组自交系群体,测定武夷山和莆田环境下水稻群体的抽穗期,并进行了QTL的定位及环境互作研究。结果表明,在武夷山环境下仅检测到一个与抽穗期相关的加性QTL,位于6号染色体上,解释了25.63%;1个位点存在显著的加性×环境互作效应,而GE互作效应对表型变异贡献几乎为0,表明控制水稻抽穗期基因的表达有显著的环境特异性。     

Genetic Variation for Salinity Tolerance in Pakistani Rice (Oryza sativa L.) Germplasm

Soil salinity is one of the major production constraints. Development and planting of salt‐tolerant varieties can reduce yield losses due to salinity. We screened 185 rice genotypes at germination stage in petri dishes under control, 50, 100 and 150 mm salt stress, and at seedling stage in Yoshida's hydroponic nutrient solution under control, 50 and 100 mm salt stress. At germination stage, 15 genotypes including Nona Bokra, Sonahri Kangni, 7421, 7423 and 7467, whereas at seedling stage, 28 genotypes including Nona Bokra, Jajai‐77, KSK‐133, KSK‐282, Fakhr‐e‐Malakand, Pakhal, IR‐6, Khushboo‐95, Shahkar and Shua‐92 were found salt tolerant. Basmati‐370, Mushkan, Homo‐46 and accessions 7436, 7437 and 7720 were sensitive to salinity at both germination and seedling stage. We further screened a subset of 33 salt‐tolerant and salt‐sensitive genotypes with SSR markers. Four SSR markers (RM19, RM171, RM172 and RM189) showed significant association with two or more of the studied traits under 50, 100 and 150 mm salt stress. These markers may be further tested for their potential in marker‐assisted selection. The salt‐tolerant genotypes identified in this study may prove useful in the development of salt‐tolerant rice varieties in adapted genetic background.     

水稻耐低磷胁迫研究进展

土壤中有效磷缺乏是制约水稻生产的主要因素之一。利用磷效率不同的水稻基因型选育磷高效水稻品种,是解决水稻磷营养问题的一种更为经济、环保的途径。本文简要论述了水稻耐低磷胁迫的机理及磷高效基因型筛选体系,重点综述了近年来水稻磷效率相关性状的QTL定位分析结果,以期为水稻耐低磷研究及磷高效水稻品种的选育提供参考。     

Inhibition of rice (Oryza sativa L.) seedling elongation by a Pseudomonas fuscovaginae toxin

Summary The effects of a Pseudomonas fuscovaginae toxin, on germination, root formation and seedling elongation, after soaking rice grains in the toxin prior to sowing, was investigated. The toxin enhanced germination, but had no apparent effect on the number of roots of the seedlings. It induced a drastic inhibition of seedlings elongation correlated to varieties susceptibility to the disease in the rice field. After denaturation of the bioactive compounds of the extract, all the previously observed effects were lost. Using the toxin and the present test, could be a reliable tool for screening genotype susceptibility to P. fuscovaginae disease.     

The use of microsatellite polymorphisms for the identification of Australian breeding lines of rice (Oryza sativa L.)

Ten microsatellite loci were analysed for 43 cultivars or breeding lines of rice. Polymorphism-Information-Content values ranged from 0.62 to 0.92. The microsatellite markers were found to be useful for cultivar identification and assessment of genetic relationships. Most of the cultivars could be uniquely identified by at least one microsatellite marker. Genetic heterogeneity was detected within rice samples by amplification of microsatellites from DNA extracted from multiple individual plants and also from bulked DNA preparations. This revised version was published online in July 2006 with corrections to the Cover Date.