粳稻野败型细胞质雄性不育恢复系SWR78的恢复基因定位

 利用野败(WA)型粳稻广亲和不育系苏秋A和广亲和广谱型恢复系SWR78配组,根据F2与BC1F1群体的育性分离情况,初步推测WA型苏秋A的育性恢复至少由3对基因控制。选取F2群体中无染色花粉植株,采用隐性基因组分析法进行恢复基因定位,将其中1个主效基因Rf4定位于第10染色体长臂上,与标记RM5629、RM5373、STS10 17和STS10 18分别相距0.17、0.03、0.03和0.07 cM。Rf4位于标记RM5373与STS10 17之间,两标记间的物理距离为78 kb。     

Effects of the number of pollen grains on cold tolerance at the booting stage in rice lines with QTLs for cold tolerance

This study was conducted to clarify the relationship between the number of pollen grains per anther and spikelet fertility under low temperature conditions in the rice cultivars and lines including lines with quantitative trait loci (QTL) for cold tolerance, adapted to the Tohoku region of northern Japan. Cold-water treatment decreased anther length, the number of pollen grains per anther, and spikelet fertility in all cultivars and lines. The number of pollen grains was proportional to anther length in all cultivars and lines and under all temperatures. Spikelet fertility decreased with decreasing the number of pollen grains in cold-water treatments at 18.5 and 19.3?°C. ‘Ouu 415’, with the qLTB3 QTL for cold tolerance, had 28% more pollen grains and 9% higher spikelet fertility than the recurrent parent, ‘Hitomebore’, in the 18.5?°C cold-water treatment, suggesting that qLTB3 increased both parameters. Lines with the qCTB8 QTL for cold tolerance had significantly more pollen grains in two of the three years and significantly higher spikelet fertility in all three years in the 19.3?°C cold-water treatment, suggesting that qCTB8 reinforced cold tolerance. Ctb1, a proposed cold-tolerance QTL, had no effect on the number of pollen grains or spikelet fertility. In conclusion, the cultivars and lines with more pollen grains had a higher cold tolerance. Some of QTLs were inferred to increase the number of pollen grains and reinforce cold tolerance.     

应用微卫星标记定位水稻恢复系密阳46的主效和微效恢复基因

应用由704个株系组成的珍汕97A/(珍汕97B/密阳46)F6测交群体,针对水稻第10染色体和第1、11染色体短臂构建了微卫星标记连锁图谱,检测到控制野败型细胞质雄性不育育性恢复的4个QTL,其中位于第10染色体长臂中下部的Rf4具有主效效应,位于第1染色体短臂的Rf3具有较大效应,位于第10染色体长臂近着丝粒处的qRf10和第11染色体短臂近着丝粒处的qRf11表现出微效作用。研究还表明,在主效基因Rf4存在时,其他3个基因仍具有提高结实率的作用,但在Rf3和Rf4同时存在时,qRf10和qRf11的效应不明显。     

Avoidance of Linkage Drag Between Blast Resistance Gene and the QTL Conditioning Spikelet Fertility Based on Genotype Selection Against Heading Date in Rice

Previous study showed that a linkage drag between a blast resistance gene Pi25(t) and QTLs conditioning spikelet fertility (qSF-6) and number of filled grains per panicle (qNFGP-6) was detected on the short arm of chromosome 6. A larger population was used for further verification, and the results confirmed the linkage drag between the blast resistance gene and QTL conditioning spikelet fertility, other than QTL conditioning number of filled grains per panicle. Breakdown or avoidance of the linkage drag could be achieved by selection against the genotype background of a heading-date gene (qHD-7) that resided in the region between RM2 and RM214 on chromosome 7. For further validation, two lines with almost identical genotypes on all chromosomal regions except the Pi25(t) region on chromosome 6 were chosen to develop a new population. The results showed that qSF-6 could be further subdivided into qSF-6-1 and qSF-6-2. When the genotype of the region between RM2 and RM214 was from rice variety Zhong 156, the linkage drag between Pi25(t) and qSF-6-2 was detected and the allele of qSF-6-2 from rice variety Gumei 2 reduced the spikelet fertility. When the genotype of the region between RM2 and RM214 was from Gumei 2, no linkage drag was detected. This indicates that the linkage drag between the blast resistance gene and the QTL conditioning spikelet fertility could be broken down or avoided under a certain background genotype selection against heading-date and provides a marker aided solution for high level of blast resistance and yield breeding in rice and other crops as well.     

Changing allele frequencies associated with specific resistance genes to leaf blast in backcross introgression lines of Khao Dawk Mali 105 developed from a conventional selection program

Key genomic regions associated with blast resistance against a broad spectrum of isolates could be identified in backcross introgression lines developed by conventional breeding program. In this article, eighty three BC₃F₂ backcross introgression lines (BILs) derived from a cross between IR68835-98-2-B-2-1-1 (a broad spectrum blast resistance variety) and KDML105 (a susceptible variety) were developed by phenotypic selection against a mixture of six virulent blast isolates (MXL) that are widely spread out in the rainfed lowland of the North and Northeast of Thailand. The resistance spectrum of the BILs was assessed by inoculating with 12 different Magnaporthe oryzae isolates that showed differential responses on the parental cultivars and the MXL that was used for phenotypic selection. All BILs showed highly resistant reactions (low disease score) to the MXL and to two blast isolates THL48 and THL149. Four markers, i.e., RM246, RM241, RM303 and RM164 completely favoring the IR68835 allele (shifting of allele frequencies from KDML105 to IR68835) were identified on chromosomes 1, 4 and 5, respectively. Therefore, these markers could be linked to the resistance genes functioning against the MXL, THL48 and THL149. Furthermore, significant shifting of alleles was identified at six markers located on chromosomes 2, 4, 8, 9 and 12. Seven DNA markers linked to specific resistance genes were identified, in which allele from IR68835 at 6 markers, i.e., RM6, RM205, RM211, RM252, RM273 and RM342 reduced disease score (DS), against blast isolates THL16, THL329, THL458, THL831, THL868 and THL96036 while allele from KDML105 at RM208 (Pi-kd on chromosomes 2) reduce DS against THL84, THL191, THL557 and THL1108. In this study, the use of DNA markers enabled the identification of specific resistance genes in the backcross breeding materials developed from routine rice breeding program through the conventional phenotypic selection. In this experiment, the usefulness of breeding materials from conventional breeding program in identifying genes corresponding to the selection was illustrated. Linked markers and their genomic location provide necessary information for further use of marker-assisted selection to improve blast resistance in rice breeding program.     

水稻籼粳杂种育性QTL定位及其效应分析

选用珍汕97B/秀水13的F2代为材料,在育性QTL分析同时,根据育成的亲籼型不育系配组的F1育性分析其QTL效应。结果表明,检测到控制花粉育性的qPF5加性效应值为-8.65,表型贡献率为11.25%。共检测到2个影响小穗育性的QTL(qSF5和qPF6),其中qSF5加性效应为-5.95,表型贡献率为9.11%,与花粉育性qPF5为同一个育性QTL;qSF6加性效应值为-8.55,表型贡献率为16.31%,为广亲和基因S5n。育成的亲籼型不育系的育性QTL(qSF6)来自籼稻等位基因或广亲和基因均可有效提高其籼粳杂种的小穗育性。此外,qSF5对后代小穗育性也有明显效应。籼粳杂种育性不仅与育性QTL有关,且受亲本籼粳成分等因素影响。     

Genetic variation in the sensitivity of anther dehiscence to drought stress in rice

Field-based screens for genetic variation in reproductive-stage drought tolerance are often confounded by genetic variation in root depth, flowering date and biomass at flowering. To reduce these confounding effects and to impose drought stress more precisely, we grew contrasting genotypes of rice (Oryza sativa L.) in shallow containers of flooded soil. When water was withheld from the shallow-rooted indica genotype IR64 for 6 days starting at −17, −7, 0, 10 and 20 days after heading (DAH), the impact on grain yield was greatest at −7 and 0DAH. The most sensitive yield component was filled grain percentage (spikelet fertility). Data on yield and spikelet fertility were also obtained for another shallow-rooted lowland indica (BRRI Dhan 31) and two deep-rooted upland tropical japonicas (Azucena and Moroberekan). Compared with well-watered controls, withholding of water for 6 days reduced spikelet fertility by ∼80% in IR64, BRRI Dhan 31 and Azucena but by 22% in Moroberekan. In a detailed comparison, water was withheld from IR64 for 5 days and from Moroberekan for 6 days, starting 3 days before the heading date of well-watered controls. Under these stress conditions, heading was delayed for 4 days in IR64 and 6 days in Moroberekan. Spikelet fertility in the top four rachis branches was reduced by 80% in IR64 and 16% in Moroberekan, a difference attributable principally to reduced anther dehiscence and lower stigma pollen density in IR64. Two properties of Moroberekan may contribute to high anther dehiscence after stress/re-watering: (i) constitutively superior development of fibrous structures in the endothecium at the anther apex and base and (ii) better maintenance of pollen size. All ovaries of Moroberekan received pollen—an average of 60 grains in well-watered plants and 42 grains in stressed/re-watered plants. In well-watered IR64, all ovaries received an average of 31 grains, whereas in stressed/re-watered IR64, 67% of ovaries received no pollen and the remainder received an average of eight grains. Moroberekan may, therefore, be a source of reproductive-stage drought tolerance through genes that maintain anther dehiscence during recovery from low water status.     

分子标记辅助选择改良C418对红莲型粳稻不育系的恢复力

【目的】高效选育红莲型(Honglian,HL)粳稻恢复系有助于HL型杂交粳稻育种,对促进三系杂交粳稻的发展具有重要的意义。【方法】Rf6是一个HL型恢复基因,来源于HL型籼稻强恢复系9311。前期研究中,在以9311为供体、日本晴为受体的一套染色体片段代换系中鉴定出携带Rf6的株系R1093。本研究利用R1093与BT型粳稻恢复系C418(携带Rf1)杂交,通过常规回交育种结合分子标记辅助选择技术,将Rf6导入C418中,进行Rf6与Rf1聚合育种;利用BT型、HL型六千辛A进行测交鉴定改良系的恢复力。【结果】共获得12个BC₃F₄株系和55个BC₄F₃株系,其中6个改良系的农艺性状已基本接近C418;测交鉴定结果表明聚合Rf6的改良系对HL型粳稻不育系的恢复度达到85%以上,可应用于水稻生产;对BT型粳稻不育系的恢复度提升效果不显著。【结论】聚合Rf6能有效改良BT型粳稻恢复系对HL型粳稻不育系恢复力,是选育HL型粳稻恢复系的一条重要途径。     

水稻印尼水田谷型细胞质雄性不育恢复系R68的恢复基因初步定位

用印尼水田谷型不育系中9A和恢复系R68配组,选取F2的高可育株和极端不育株构建2个基因池,用82个完全不育单株作为定位群体,利用分布于12条染色体的413对SSR引物对双亲和两池进行多态性分析。 位于第1染色体的RM283和位于第10染色体的RM5756、RM258、RM6100、RM171 在亲本、两池间存在多态性,用F2单株验证证明它们与恢复基因连锁。经典遗传分析和分子标记定位研究表明,印尼水田谷型细胞质雄性不育恢复系R68具有2对恢复基因,分别位于第1和第10染色体上。位于第1染色体的恢复基因与分子标记RM283的距离是6.7 cM,位于第10染色体的恢复基因与标记RM5756、RM258、RM6100和RM171间的距离分别是10.4、8.0、2.4和4.2 cM。     

Screening for Spikelet Fertility and Validation of Heat Tolerance in a Large Rice Mutant Population

A total of 10 000 M4 individuals in Jao Hom Nil (JHN) mutant population was treated with high temperature (40 ℃ to 45 ℃) during the day time (6 h) from the booting to the harvesting stages, and ambient temperature (33 ℃ to 35℃) was used as the control. The results of screening and yield trials found that the mutant line M9962 had a high spikelet fertility of 78% under heat stress. In addition, the other mutant lines, including M3181 and M7988, had a spikelet fertility of approximately 70%. However, the JHN wild type, Sin Lek, RD15 and RD33 had very low spikelet fertility of 34%, 14%, 9% and 4%, respectively. The lower spikelet fertility at an elevated temperature resulted in a dramatic decrease of filled grain and contributed to a loss in 100-grain weight. M9962 is a potential genetic stock for use in a heat tolerance breeding programme. In addition, spikelet fertility at high temperature was representative of heat tolerance and can be used as a screening trait for heat tolerance during the reproductive phase on a large scale.     

早红突A不同穗位颖花花粉育性的变异

从6月11日至7月2日连续观察早红突A花粉育性的变化动态，不同时期镜检结果表明，染色花粉频率呈现较大变（27．1％－92．3％），染色花粉数与颖花着生的部位有密切关系。其中，第4枝梗染色花粉频率相对较高，第6枝梗单位颖花内染色花粉数最多；染色花粉频率和所含染色花粉数随着枝梗位置上升有逐步递增的趋势，相关分别达显著（0．852 6^*）和极显著水平（0．911 9^**）；每一枝梗基部1－4朵颖花（第1镜检单位）含染色花粉数和染色花粉频率一般高于同枝梗其它颖花，并从枝梗基部往上逐步递减。染色花粉数的增加与镜检前10d日平均气温和最低气温分别呈显著和极显著正相关，表明它对高温有较强的敏感性。讨论了单株选择对花粉育性的影响。     

水稻籼粳杂种育性的QTL分析

 以籼稻保持系珍汕97B和粳稻保持系辽91B为亲本,构建了一个包含176个单株的F2群体及123个SSR标记的遗传图谱,在3种环境下联合检测控制花粉育性和小穗育性的QTL。共检测到3个控制花粉育性的主效应（加性效应和显性效应）QTL（qPF3、qPF5和qPF6）和4个控制小穗育性的主效应QTL（qSF3、qSF5、qSF6和qSF8）,其中qPF5与qSF5、qPF6与qSF6均为同一个QTL,为重要的育性QTL。另外,检测到3对花粉育性和4对小穗育性QTL间互作,说明上位性效应对籼粳杂交后代的育性具有重要作用。     

通过生育期基因型选择避免稻瘟病抗性与结实率的遗传累赘

利用重组自交系研究表明,在水稻第6染色体短臂上稻瘟病抗性基因Pi25(t)与控制结实率和每穗实粒数的QTL之间存在遗传累赘。为了验证这种关系,采用了更大的遗传群体进行分析,结果表明稻瘟病抗性与结实率存在遗传累赘,但未检测到稻瘟病抗性与每穗实粒数存在遗传累赘。通过对第7染色体长臂RM2-RM214区间抽穗期基因（qHD 7）型背景进行选择,可以打破或避免稻瘟病抗性与结实率的遗传累赘。为了进一步验证这种关系,选择Pi25(t)区间基因型不同、RM2-RM214区间基因型相同、其他染色体区间基本一致的两个株系发展新群体进行分析,除第6染色体的结实率QTL可以分解成2个效应较小的QTL（qSF 6 1和qSF 6 2）外,当第7染色体RM2-RM214区间基因型为中156背景时,Pi25(t)与结实率QTL（qSF 6 2）存在遗传累赘,且qSF 6 2来自父本谷梅2号的等位基因起减效作用;当第7染色体RM2-RM214区间基因型为谷梅2号背景时,第6染色体上没有检测到结实率QTL。上述结果说明在特定育种材料中对抽穗期基因进行选择可以成功打破或避免稻瘟病抗性与结实率的遗传累赘,为水稻以及其他作物的高产抗病育种提供了一种新途径。     

Development of introgression lines of an Indica-type rice variety, IR64, for unique agronomic traits and detection of the responsible chromosomal regions

A total of 334 introgression lines (INLs: BC₃-derived lines) derived from crosses between a recurrent parent of Indica rice cultivar IR64 and 10 donor parents, including new plant type (NPT) lines IR65600-87-2-2-3, IR65598-112-2, IR65564-2-2-3, IR69093-41-2-3-2, IR69125-25-3-1-1, Hoshiaoba, IR66215-44-2-3, IR68522-10-2-2, IR71195-AC1, and IR66750-6-2-1, have been developed. These INLs with IR64 genetic background were characterized for eight agronomic traits: days to heading, culm length, leaf width, leaf length, panicle length, panicle number, 100-grain weight, and total spikelet number per panicle at the International Rice Research Institute from 2005 to 2007. To identify introgressed segments from the donor parents, genotypes of the 334 INLs were detected using more than 200 polymorphic simple sequence repeat markers. These segments detected on chromosomes 1, 2, 4, 5, and 6 were commonly introgressed across the INLs from more than four donor varieties. Based on the data of phenotype and genotype for the 334 INLs, associations between agronomic traits and introgressed chromosomal segments in the 334 INLs were investigated. A total of 54 regions for the eight traits were detected: seven regions for days to heading, eight regions for culm length, eight regions for leaf width, four regions for leaf length, six regions for panicle length, three regions for panicle number per plant, seven regions for 100-grain weight, and 11 regions for total spikelet number per panicle. Among them, the region on the long arm of chromosome 4 was associated with characteristics of the NPT such as long leaf, broad leaf, and high spikelet number. The developed 334 INLs with the IR64 genetic background will be useful materials for genetic analysis of agronomic traits.     

Mapping of Rice Fertility-Restoring Genes for ID-Type Cytoplasmic Male Sterility in a Restorer Line R68

An F2 population derived from the cross Zhong 9NR68 was used to map the fertility-restoring (Rf) gene for ID-type cytoplasmic male sterility (CMS).Two bulks (a fertile bulk and a sterile bulk) were constructed by pooling equal amount of ten highly fertile lines and ten highly sterile lines,respectively.Four hundred and thirteen pairs of simple sequence repeat (SSR) primers,which evenly distributed on 12 chromosomes of rice,were selected for analyzing polymorphisms between the parents and between the two bulks.The primer RM283 on chromosome 1 and the primers RM5756,RM258,RM6100 and RM171 on chromosome 10 were found to be polymorphic between the parents and between the two bulks.These five SSR markers were linked to fertility-restoring genes.A total of 82 excessive sterile lines were selected from Zhong 9NR68 F2 population to estimate the genetic distance between five SSR markers and fertility-restoring genes respectively.The results indicated that one Rf gene was linked to RM283 located on chromosome 1 at a distance of 6.7 cM,and the other Rfgene was mapped to the long arm of chromosome 10 flanked by RM258 and RM6100 at the distances of 8.0 cM and 2.4 cM,respectively.     

粳稻发芽期耐碱性的QTL检测

 以粳粳交高产106/长白9号的200个F2:3株系为作图群体,在0.15% Na2CO3溶液碱胁迫下,进行了水稻发芽率及其相对碱害率的鉴定评价,并以SSR标记构建的分子连锁图谱为基础,对水稻发芽率及其相对碱害率进行了数量性状基因座(QTL)检测。结果表明,在F3株系群中水稻发芽率及其相对碱害率均呈单峰接近正态的连续分布。共检测到碱胁迫下与水稻发芽率相关的QTL 7个,对表型变异的贡献率范围为4.05%～12.61%,其中位于第6染色体RM225-RM204区间的qGC 6和位于第9染色体RM219-RM3700区间的qGC 9对表型变异的贡献率分别为12.61%和10.85%。共检测到与水稻发芽率相对碱害率相关的QTL 6个,对表型变异的贡献率为4.82%～28.07%,其中位于第2染色体RM29-RM221区间的qRGC 2、位于第6染色体RM225-RM204区间的qRGC 6 1、位于第9染色体RM219-RM3700区间的qRGC 9和位于第12染色体RM260-RM3226区间的qRGC 12对表型变异的贡献率较大,分别为28.07％、15.35％、15.61％和18.91％,为主效QTL,但其相应的区间距离均较远,需要进一步深入研究。所检测的QTL增效等位基因主要表现为部分显性和超显性。     

Yield Traits and Associated Marker Segregation in Elite Introgression Lines Derived from O. sativa × O. nivara

Introgression lines (ILs) derived from interspecific crosses are a source of new genetic variability. A total of 55 ILs derived from two crosses Swarna × O. nivara IRGC81848 (population A) and Swarna × O. nivara IRGC81832 (population B) were characterized for yield and yield-related traits/QTLs. Segregation of 103 simple sequence repeat (SSR) markers associated with yield-related QTLs was studied. Population A showed an average of 12.6% homozygous O. nivara alleles and population B showed 10.6%. Interestingly, three SSR markers, RM223, RM128 and RM517, showed conspicuous pattern of segregation. The distribution of parental alleles at three loci RM223, RM128 and RM517 linked to yield-related traits was unique. These markers flanked to several yield-related QTLs. RM223, flanking to qyld8.3, was heterozygous in almost all the 55 ILs except in IL10-3S and IL131S. RM128 on chromosome 1 and RM517 on chromosome 3 were mutually exclusive in 46 out of 55 ILs. These 46 ILs showed either of the marker allele RM128 or RM517 from O. nivara but not both. IL166S had both RM128 and RM517 from O. nivara and the other ILs showed homozygous Swarna allele at RM517 except IL65S. Population structure assigned the 55 ILs to three sub-populations based on their genomic diversity. IL65S, IL166S, IL248S, IL7K and IL250K showed high yields in multi-location trials, and IL248S was released for cultivation as DRRDhan 40.     

水稻单片段代换系对两种不育细胞质恢复性的遗传分析

 由华南农业大学植物分子育种实验室选育的水稻单片段代换系S42对野败型（WA型）和夜公型（Y型）细胞质雄性不育系均具有较强的恢复性。以野败型不育系珍汕97A和Y型不育系Y华农A为母本,单片段代换系S42为父本进行杂交,采用分子标记辅助选择和连续回交的方法构建了两个BC3F2群体。利用与第1、10染色体上恢复基因Rf3和Rf4两侧紧密连锁的SSR标记,从这两个BC3F2群体中筛选携带有基因型Rf3Rf3/rf4rf4和rf3rf3/Rf4Rf4的单株,对这些单株进行花粉和小穗育性观察,并利用205个多态性SSR标记对这些单株进行遗传背景分析,结果表明： 1）在同一细胞核背景下（S42）,WA型不育细胞质的可恢复性好于Y型不育细胞质,单片段代换系S42中的恢复基因Rf4的恢复力大于Rf3; 2）单片段代换系S42中的恢复基因对于珍汕97A和Y华农A表现出质量 数量性状的遗传。在单片段代换系S42中,除了主效恢复基因Rf3和Rf4外,微效基因或者修饰基因也表现出对珍汕97A和Y华农A的育性恢复作用,而且效应较大; 3）在构建的两个BC3F2群体中,基因型Rf3Rf3/rf4rf4和rf3rf3/Rf4Rf4单株的遗传背景片段数平均为1.1,对应于恢复基因Rf3和Rf4座位的代换片段平均长度分别为14.5  cM 和17.4  cM。     

New Temperature Sensitive Genic Male Sterile Lines with Better Outcrossing Ability for Production of Two-Line Hybrid Rice

An investigation was carried out with three newly developed temperature sensitive genic male sterile(TGMS) lines for their floral traits, seed production potential and outcrossing ability in ten cross combinations. In the TGMS lines, fertile pollens had an average diameter of 0.89 mm while the sterile pollens was with 0.02 mm diameter.TS-29-150 GY produced the biggest fertile pollens with 0.92 mm and other two lines produced relatively smaller pollens with 0.91 and 0.85 mm. Pollen fertility during the fertility reversion period was an average of 60.7%. TS-29-150 GY had the maximum of 66.9% spikelet fertility whereas other two lines(TNAU18S and TNAU60S) had relatively lower spikelet fertility of 27.8% and 26.7%, respectively.Average of 17.00 g of seed yield was obtained in the TGMS lines during the fertility reversion period. TS-29-150 GY had the highest value of 21.20 g of seed yield while TNAU18 S and TNAU60 S produced 16.6 g and13.2 g of seed yield, respectively. The low seed production ability of these three TGMS lines was attributed only to the environmental conditions prevailing during the period. All three TGMS lines had considerable outcrossing potential of 41.2%, 24.6% and 25.0%, respectively. The cross combinations viz.TNAU18S/IET21508(36 g/plant), TNAU18S/IET21044(13 g/plant), TNAU18S/IET21009(26.5 g/plant),TNAU60S/CB-09-106(26.2 g/plant), TNAU60S/IET21009(14 g/plant) and TS29-150-GY/DRR 3306(39.2g/plant) showed perfect synchronization with acceptable hybrid seed yield, indicating suitability of TGMS system under Indian condition. Based on the outcrossing related traits viz. panicle exertion, angle of glume opening, stigma length and pollen size, TNAU18 S was identified as the best, followed by TS-29-150 GY.     

Haplotyping of Rice Genotypes Using Simple Sequence Repeat Markers Associated with Salt Tolerance

Salt stress is a major problem in most of the rice growing areas in the world. A major QTL Saltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice. This study aimed to characterize the haplotype diversity at Saltol and additional QTLs associated with salt tolerance. Salt tolerance at the seedling stage was assessed in 54 rice genotypes in the scale of 1 to 9 score at EC = 10 d Sm-1 under controlled environmental conditions. Seven new breeding lines including three KMR3/O. rufipogon introgression lines showed similar salt tolerant ability as FL478 and can be good sources of new genes/alleles for salt tolerance. Simple sequence repeat(SSR) marker RM289 showed only two alleles and RM8094 showed seven alleles. Polymorphic information content value varied from 0.55 for RM289 to 0.99 for RM8094 and RM493. Based on 14 SSR markers, the 54 lines were clearly separated into two major clusters. Fourteen haplotypes were identified based on Saltol linked markers with FL478 as the reference. Alleles of RM8094 and RM3412 can discriminate between the salt tolerant and susceptible genotypes clearly and hence can be useful in marker-assisted selection at the seedling stage. Other markers RM10720 on chromosome 1 and RM149 and RM264 on chromosome 8 can also distinguish tolerant and susceptible lines but with lesser stringency.