Dissection of genetic overlap of drought and low-temperature tolerance QTLs at the germination stage using backcross introgression lines in soybean

Northeast of China is the main soybean production area, drought and low-temperature tolerance are both main factors involved in reducing soybean yield and limiting planting regions, the most effective way to solve this problem is to breed cultivars with drought and low-temperature tolerance. A set of the BC₂F₃ lines was constructed with Hongfeng 11 as recurrent parent and Harosoy as donor parent, and screened in drought and low-temperature condition at the germination stage. Related QTLs were obtained by Chi-test and ANOVA analysis with genotypic and phenotypic data. Eighteen QTLs of drought tolerance and 23 QTLs of low-temperature tolerance were detected. Among them, 12 QTLs were correlated with both drought and low-temperature tolerance, which showed a partial genetic overlap between drought and low-temperature tolerance at the germination stage in soybean. Among the 12 genetic overlap QTLs, Satt253, Satt513, Satt693, Satt240, Satt323, and Satt255 were detected by at least one method for both drought and low-temperature tolerance. Satt557, Satt452, Sat_331, Satt338, Satt271, and Satt588 were detected by only one analysis method. The QTLs detected above were significant loci for drought or low-temperature tolerance in soybean. This will play an important role in MAS for development of both drought and low-temperature tolerance variety.     

A novel functional gene associated with cold tolerance at the seedling stage in rice

Identification and cloning of cold‐tolerant genes that can stably express under different cold environments are crucial for molecular rice breeding for cold tolerance. In the previous study, we identified a cold‐tolerant QTL at the seedling stage, qCTS‐9 which could be detected under different cold environments using a recombinant inbred line (RIL) population derived from a cold‐tolerant variety Lijiangxintuanheigu (LTH) and a cold‐sensitive variety Shanhuangzhan 2 (SHZ‐2). In this study, eight candidate genes within the qCTS‐9 interval were identified through integrated analysis of QTL mapping with genomewide differential expression profiling of LTH. The qRT‐PCR assay showed that only Os09g0410300 exhibited different expression patterns between LTH and SHZ‐2 during cold stress, and significantly positive correlation was found between cold induction of Os09g0410300 and seedling cold tolerance in the RI lines. Five SNPs and one InDel in the promoters of Os09g0410300 were detected between LTH and SHZ‐2, and the InDel marker ID410300 designed based on the insertion–deletion polymorphism in the promoter was significantly associated with seedling cold tolerance in RIL population. Further, Os09g0410300 over‐expression plants exhibited enhanced cold tolerance at the seedling stage compared with the wild‐type plants. Thus, our results suggest that Os09g0410300 is the functional gene underlying qCTS‐9. To our knowledge, it is a novel gene contributed to enhance cold tolerance at the seedling stage in rice. Identification of the functional gene underlying qCTS‐9 and development of the gene‐specific marker will facilitate molecular breeding for cold tolerance at the seedling stage in rice through transgenic approach and marker‐assisted selection (MAS).     

Mapping QTLs conferring salt tolerance during germination in tomato by selective genotyping

This study was conducted to identify genomic regions (quantitative trait loci, QTLs) affecting salt tolerance during germination in tomato. Germination response of an F2 population of a cross between UCT5 (Lycopersicon esculentum, salt-sensitive) and LA716 (L. pennellii, salt-tolerant) was evaluated at a salt-stress level of 175 mM NaCl + 17.5 mM CaCl2 (water potential ca. –950 kPa). Germination was scored visually as radicle protrusion at 6 h intervals for 30 consecutive days. Individuals at both extremes of the response distribution (i.e., salt-tolerant and salt-sensitive individuals) were selected. The selected individuals were genotyped at 84 genetic markers including 16 isozymes and 68 restriction fragment length polymorphisms (RFLPs). Trait-based marker analysis (TBA) which measures changes (differences) in marker allele frequencies in selected lines was used to identify marker-linked QTLs. Eight genomic regions were identified on seven tomato chromosomes bearing genes (QTLs) with significant effects on this trait. The results confirmed our previous suggestion that salt tolerance during germination in tomato is polygenically controlled. The salt-tolerant parent contributed favorable QTL alleles on chromosomes 1, 3, 9 and 12 whereas the salt sensitive parent contributed favorable QTL alleles on chromosomes 2, 7 and 8. The identification of favorable alleles in both parents suggests the likelihood of recovering transgressive segregants in progeny derived from these parental genotypes. The results can be used for marker-assisted selection and breeding of salt-tolerant tomatoes.     

Root and shoot traits responses to phosphorus deficiency and QTL analysis at seedling stage using introgression lines of rice

Phosphorous （P） deficiency is a major restraint factor for crop production and plants have developed several mechanisms to adapt to low P stress. In this study, a set of 271 introgression lines （ILs） were used to characterize the responses of seedlings to low P availability and to identify QTLs for root traits, biomass, and plant height under P-deficiency and P-sufficiency conditions. Plant height, total dry weight, shoot dry weight, and root number were inhibited under P-deficiency, whereas maximum root length （MRL） and root-shoot ratio （RS） were induced by P-deficiency stress. Relative MRL （RMRL, the ratio of MRL under P-deficiency to MRL under P-sufficiency con- dition） and relative RS （RRS） were used to evaluate P-deficiency tolerance at the seedling stage. A total of 24 additive QTLs and 29 pairs of epistatic QTLs were detected, but only qRN4 was detected in both conditions. This suggested that different mechanisms may exist in both P supply levels. QTLs for adaptive traits （RMRL, RRS, RRV, and RRDW） and qRN4 consistently expressed to increase trait stability may contribute to P-deficiency tolerance. Twelve intervals were cluster regions of QTLs for P-deficiency tolerance, and one QTL （qRRSS） showed pleiotropic effects on P-deficiency tolerance and drought tolerance. These interesting QTLs can be used in marker-assisted breeding through the target ILs.     

Physiological and genetic mapping study of tolerance to root-knot nematode in rice

The root-knot nematode Meloidogyne graminicola is an obligate biotrophic parasite and a major pest of rice (Oryza sativa) for which resistant varieties are not currently available. Quantitative trait loci (QTLs) for partial resistance to M. graminicola were identified using a mapping population based on two rice varieties, Bala x Azucena. Experiments were carried out to investigate the interactions between M. graminicola and these two varieties in terms of nematode establishment, reproduction and effect on rice yield. Nematode establishment was also assessed in the mapping population. Meloidogyne graminicola consistently caused more galling and had higher reproductive success in Azucena than in Bala. M. graminicola did not significantly reduce yield in Bala, but caused a yield reduction of almost half in Azucena, suggesting that the partial resistance to nematode establishment was related to nematode tolerance. A total of six significant or putative QTLs for nematode tolerance were detected. For two of the QTLs detected, Azucena was the donor of the tolerance alleles, suggesting it may be possible to breed plants with greater tolerance than Bala.     

Mapping QTLs for heading synchrony in a doubled haploid population of rice in two environments

Simultaneous heading of plants within the same rice variety, also refer to heading synchrony, is an important factor that affects simultaneous ripening of the variety. Understanding of the genetic basis of heading synchrony may contribute to molecular breeding of rice with simultaneous heading and ripening. In the present study, a doubled haploid （DH） population, derived from a cross between Chunjiang 06 and TN1 was used to analyze quantitative trait locus （QTL） for heading synchrony related traits, i.e., early heading date （EHD）, late heading date （LHD）, heading asynchrony （HAS）, and tiller number （PN）. A total of 19 QTLs for four traits distributed on nine chromosomes were detected in two environments. One QTL, qHAS-8 for HAS, explained 27.7% of the phenotypic variation, co-located with the QTLs for EHD and LHD, but it was only significant under long-day conditions in Hangzhou, China. The other three QTLs, qHAS-6, qHAS-9, and qHAS-10, were identified under short-day conditions in Hainan, China, each of which explained about 11% of the phenotypic variation. Two of them, qHAS-6 and qHAS-9, were co-located with the QTLs for EHD and LHD. Two QTLs, qPN-4 and qPN-5 for PN, were detected in Hangzhou, and qPN-5 was also detected in Hainan. However, none of them was co-located with QTLs for EHD, LHD, and HAS, suggesting that PN and HAS were controlled by different genetic factors. The results of this study can be useful in marker assisted breeding for improvement of heading synchrony.     

Importance of over-dominance as the genetic basis of heterosis in rice

In populations derived from commercial hybrid rice combination Shanyou 10, F1 hetero-sis and F2 inbreeding depression were observed on grain yield (GYD) and number of panicles (NP). Using marker loci evenly distributed on the linkage map as fixing factors, the F2 population was divided into sub-populations. In a large number of sub-populations, significant correlations were observed between heterozygosity and GYD, and between heterozygosity and NP. This was especially true in type III sub-populations in which the genotype of a fixing factor was heterozy-gotes. In type III sub-populations, 15 QTL for GYD and 13 QTL for NP were detected, of which the majority exhibited over-dominance effects for increasing the trait values. This study showed that over-dominance played an important role in the genetic control of heterosis in rice.     

Quantitative trait loci for cold tolerance of rice recombinant inbred lines in low temperature environments

Low temperature is one of the major environmental stresses in rice cultivation in high-altitude and high-latitude regions. In this study, we cultivated a set of recombinant inbred lines (RIL) derived from Dasanbyeo (indica) / TR22183 (japonica) crosses in Yanji (high-latitude area), Kunming (high-altitude area), Chuncheon (cold water irrigation) and Suwon (normal) to evaluate the main effects of quantitative trait loci (QTL) and epistatic QTL (E-QTL) with regard to their interactions with environments for cold-related traits. Six QTLs for spikelet fertility (SF) were identified in three cold treatment locations. Among them, four QTLs on chromosomes 2, 7, 8, and 10 were validated by several near isogenic lines (NILs) under cold treatment in Chuncheon. A total of 57 QTLs and 76 E-QTLs for nine cold-related traits were identified as distributing on all 12 chromosomes; among them, 19 QTLs and E-QTLs showed significant interactions of QTLs and environments (QEIs). The total phenotypic variation explained by each trait ranged from 13.2 to 29.1% in QTLs, 10.6 to 29.0% in EQTLs, 2.2 to 8.8% in QEIs and 1.0% to 7.7% in E-QTL × environment interactions (E-QEIs). These results demonstrate that epistatic effects and QEIs are important properties of QTL parameters for cold tolerance at the reproductive stage. In order to develop cold tolerant varieties adaptable to wide-ranges of cold stress, a strategy facilitating marker-assisted selection (MAS) is being adopted to accumulate QTLs identified from different environments.     

小麦萌发期抗旱和耐盐性状的QTL分析

该研究以‘山农0431×鲁麦21’RIL群体及其父母本为材料,用20%PEG-6000溶液和100 mmol·L-1 NaCl溶液分别模拟干旱和盐环境,对12个小麦萌发期抗旱耐盐相关性状进行测定,结合已构建的分子标记遗传图谱对小麦萌发期抗旱、耐盐的相关性状进行QTL分析,为小麦抗旱、耐盐基因的克隆和分子标记辅助选择提供参考。结果表明:(1)正常、干旱和盐胁迫3种处理下共检测到143个QTL。检测到相对高频QTL(RHF-QTL)29个,平均贡献率范围为4.39%~13.28%,贡献率在10%以上的主效RHF-QTL有10个。(2)检测到胁迫下特异表达的RHF-QTL共17个,正常处理下特异表达的RHF-QTL为8个,稳定表达的RHF-QTL为4个。(3)QTL分析结果表明,7个RHF-QTL形成了3个QTL簇,且分布在2D、4D和5B等3条染色体上,其中:QC1位于2D染色体的wPt-6847~D-1172783区间,包括3个QTL(QRl-2D.2、QSdw-2D.3、QTdw-2D);QC2位于4D染色体短臂的D-2245724~D-1108531区间,包括2个QTL(QSl-4D、QShl-4D);QC3位于5B染色体的D-982263~S-1083095区间,包括2个QTL(QSl-5B.2、QTdw-5B.1)。     

水稻苗期耐盐突变体的遗传分析及基因定位

在籼稻品种R401辐射诱变的M2群体中筛选到一个苗期耐盐突变体, 在150 mmol/L的NaCl溶液处理下对照植株枯萎死亡, 而突变体植株依然存活。以粳稻品种Nipponbare(不耐盐)和耐盐突变体作亲本, 构建了一个F2群体, 调查该群体在150 mmol/L的NaCl溶液胁迫下的表现, 发现Nipponbare和耐盐突变体苗期耐盐性的差异受单个主基因控制, 耐盐为隐性, 将该基因暂时命名为SST(t)。利用该F2群体, 采用集团分离分析(Bulked segregant analysis, BSA)法将SST(t)定位在第6染色体上, 进一步对F2群体中137个典型的耐盐单株的分子标记进行分析, 将该基因定位在InDel标记ID26847和ID27253之间, 约2.3 cM (或406 kb)的区间内, 与两标记分别相距1.2 cM和1.1 cM。     

Analysis of quantitative trait loci underlying the traits related to chlorophyll content of the flag leaf in rice

A population of 117 doubled haploid (DH) lines derived from the cross of Zhaiyeqing 8 (indica) x Jingxi 17 (japonica) was employed to map quantitative trait loci (QTL) underlying four physiological traits related to chlorophyll contents of the flag leaf. There were significantly positive correlations among chlorophyll a, chlorophyll b and chlorophyll a+ b content. Chlorophyll a/b ratio was significantly negatively correlated with chlorophyll b content. These four traits were normally distributed with transgressive segregation, suggesting that they were controlled by multiple minor genes. A total of 11 QTLs were detected for the four traits and they lay on six chromosomes. Each of them explained 9.2%-19.6% of the phenotypic variations, respectively. Of these, two QTLs controlling chlorophyll a content were mapped on chromosomes 2 and 5; four QTLs underlying chlorophyll b content were mapped on chromosomes 2, 3, 5 and 9; three QTLs underlying chlorophyll a+b amount were mapped on chromosomes 3, 5 and 9; two QTLs under-lying chlorophyll a/b ratio were mapped on chromosomes 6 and 1 1. The intrinsic relationship among the four traits and the practical implication in rice breeding are discussed.     

Analysis of quantitative trait loci underlying the traits related to chlorophyll content of the flag leaf in rice

A population of 117 doubled haploid (DH) lines derived from the cross of Zhaiyeqing 8 (indica)× Jingxi 17 (japonica) was employed to map quantitative trait loci (QTL) underlying four physiological traits related to chlorophyll contents of the flag leaf. There were significantly positive correlations among chlorophyll a, chlorophyll b and chlorophyll a + b content. Chlorophyll a/b ratio was significantly negatively correlated with chlorophyll b content. These four traits were normally distributed with transgressive segregation, suggesting that they were controlled by multiple minor genes. A total of 11 QTLs were detected for the four traits and they lay on six chromosomes. Each of them explained 9.2%–19.6% of the phenotypic variations, respectively. Of these, two QTLs controlling chlorophyll a content were mapped on chromosomes 2 and 5; four QTLs underlying chlorophyll b content were mapped on chromosomes 2, 3, 5 and 9; three QTLs underlying chlorophyll a + b amount were mapped on chromosomes 3, 5 and 9; two QTLs underlying chlorophyll a/b ratio were mapped on chromosomes 6 and 11. The intrinsic relationship among the four traits and the practical implication in rice breeding are discussed. __________ Translated from Journal of Wuhan University (Science Edition), 2006, 52(6): 751–756 [译自: 武汉大学学报(理学版)]     

生物炭调控盐胁迫下水稻幼苗耐盐性能

土壤盐渍化降低土壤生产力.探索生物炭对盐胁迫下水稻幼苗耐盐性能的影响,对调控盐渍区水稻生产潜力具有重要意义.本研究通过生物炭介入盐胁迫稻田土壤的盆栽试验,调查了生物炭对盐胁迫下土壤环境和水稻幼苗耐盐性能的影响.盐胁迫设置4个水平,分别为0 g NaCl·kg-1土(S0),1 g NaCl·kg-1土(S1),2 g ...     

Toward understanding genetic mechanisms of complex traits in rice

Rice is the primary carbohydrate staple cereal feeding the world population. Many genes, known as quantitative trait loci (QTLs), con-trol most of the agronomically important traits in rice. The identification of QTLs controlling agricultural traits is vital to increase yield and meet the needs of the increasing human population, but the progress met with challenges due to complex QTL inheritance. To date,many QTLs have been detected in rice, including those responsible for yield and grain quality; salt, drought and submergence tolerance;disease and insect resistance; and nutrient utilization efficiency. Map-based cloning techniques have enabled scientists to successfully fine map and clone approximately seventeen QTLs for several traits. Additional in-depth functional analyses and characterizations of these genes will provide valuable assistance in rice molecular breeding.     

应用二种定位法比较不同世代水稻产量性状QTL的检测结果

应用珍汕97B／密阳46的F2和重组自交系（RIL）群体,建立RFLP连锁图,检测控制稻谷产量及其5个构成因子的QTL。结果表明,具有较大加性效应者,能同时在F2和RIL群体中检测到。而且,在重组自交系群体中,发现设重复的表型鉴定与基于单株的表型鉴定,对效应较高的QTL的检测影响不大。     

Identification of QTLs for root characteristics in maize grown in hydroponics and analysis of their overlap with QTLs for grain yield in the field at two water regimes

We investigated the overlap among quantitative trait loci (QTLs) in maize for seminal root traits measured in hydroponics with QTLs for grain yield under well-watered (GY-WW) and water-stressed (GY-WS) field conditions as well as for a drought tolerance index (DTI) computed as GY-WS/GY-WW. In hydroponics, 11, 7, 9, and 10 QTLs were identified for primary root length (R1L), primary root diameter (R1D), primary root weight (R1W), and for the weight of the adventitious seminal roots (R2W), respectively. In the field, 7, 8, and 9 QTLs were identified for GY-WW, GY-WS, and DTI, respectively. Despite the weak correlation of root traits in hydroponics with GY-WW, GY-WS, and DTI, a noticeable overlap between the corresponding QTLs was observed. QTLs for R2W most frequently and consistently overlapped with QTLs for GY-WW, GY-WS, and/or DTI. At four QTL regions, an increase in R2W was positively associated with GY-WW, GY-WS, and/or DTI. A 10 cM interval on chromosome 1 between PGAMCTA205 and php20644 showed the strongest effect on R1L, R1D, R2W, GY-WW, GY-WS, and DTI. These results indicate the feasibility of using hydroponics in maize to identify QTL regions controlling root traits at an early growth stage and also influencing GY in the field. A comparative analysis of the QTL regions herein identified with those described in previous studies investigating root traits in different maize populations revealed a number of QTLs in common.     

RFLP mapping of major and minor genes for important agronomic characters in rice

A molecular genetic map with 233 RFLP markers which covered about 2070 cM of rice genome was constructed based on a doubled haploid (DH) population derived from anther culture of a cross between an indica variety Gui630 and a japonica variety 02428. Quantitative trait loci (QTLs) for agronomic characters such as number of panides, heading date, plant height, number of spikelets, number of grains, fertility and 1 000-grain weight were analyzed using interval mapping approach. 8 major genes and 29 minor genes were identified associating with these traits. The results also indicated that great phenotypic difference between parents was profitable in detection of major genes.     

A 3-Mbp fragment on rat chromosome 1 affects susceptibility both to stroke and kidney injury under salt loading in the stroke-prone spontaneously hypertensive rat: a genetic approach using multiple congenic strains

We have previously reported that a major quantitative trait locus (QTL) responsible for susceptibility to salt-induced stroke in the stroke-prone spontaneously hypertensive rat (SHRSP) is located in a 3-Mbp region on chromosome 1 covered by SHRSP.SHR-(D1Rat23-D1Rat213)/Izm (termed Pr1.31), a congenic strain with segments from SHRSP/Izm introduced into the stroke-resistant SHR/Izm. Here, we attempted to narrow down the candidate region on chromosome 1 further through analyses of subcongenic strains constructed for the target region. Simultaneously, salt-induced kidney injury was evaluated through the measurement of urinary albumin and the gene expression of renal tubular injury markers (Kim-1 and Clu) to explore a possible mechanism leading to the onset of stroke. All subcongenic strains examined in this study showed lower susceptibility to salt-induced stroke than SHRSP. Interestingly, Pr1.31 had the lowest stroke susceptibility when compared with newly constructed subcongenic strains harboring fragments of the congenic sequence in Pr1.31. Although Kim-1 and Clu expression after 1 week of salt loading in Pr1.31 did not differ significantly from those in SHRSP, the urinary albumin level of Pr1.31 was significantly lower than those of the other subcongenic strains and that of SHRSP. The present results indicated that, although the congenic fragment in Pr1.31 harbored the gene(s) related to salt-induced organ damages, further genetic dissection of the candidate region was difficult due to multiple QTLs suggested in this region. Further analysis using Pr1.31 will unveil genetic and pathophysiological mechanisms underlying salt-induced end organ damages in SHRSP.     

大豆耐盐相关QTLs鉴定和功能基因研究进展

大豆(Glycine max (L.) Merill)是重要的粮食作物和经济作物,盐胁迫能造成大豆产量的大幅度降低。本文综述了通过正向遗传学手段获得的大豆耐盐数量性状位点(Quantitative trait locus, QTL)以及通过反向遗传学方法获得的大豆耐盐功能基因方面的研究进展。目前,正向遗传学发掘基因主要有图位克隆(Map-based cloning)和全基因组关联分析(Genome-wide association study, GWAS)两种方案,其中通过图位克隆在大豆中已经获得了6个耐盐QTL位点并且定位了1个重要的耐盐基因;利用GWAS在大豆中获得了1个耐盐功能基因。利用反向遗传学在大豆中获得了大量的耐盐相关功能基因并在模式植物中验证了其功能,主要包括离子转运蛋白基因和转录因子基因。这些研究为揭示大豆耐盐分子机制以及通过分子标记辅助育种或转基因技术创制耐盐大豆奠定了基础。     

RFLP mapping of QTLs conferring salt tolerance during the vegetative stage in tomato

 Quantitative trait loci (QTLs) contributing to salt tolerance during the vegetative stage in tomato were investigated using an interspecific backcross between a salt-sensitive Lycopersicon esculentum breeding line (NC84173, maternal and recurrent parent) and a salt-tolerant Lycopersicon pimpinellifolium accession (LA722). One hundred and nineteen BC₁ individuals were genotyped for 151 RFLP markers and a linkage map was constructed. The parental lines and 119 BC₁S₁ families (self-pollinated progeny of the BC₁ individuals) were evaluated for salt tolerance in aerated saline-solution cultures with the salt concentration gradually raised to 700 mM NaCl+70 mM CaCl₂ (equivalent to an electrical conductivity of approximately 64 dS/m and a water potential of approximately −35.2 bars). The two parental lines were distinctly different in salt tolerance: 80% of the LA722 plants versus 25% of the NC84173 plants survived for at least 2 weeks after the final salt concentration was reached. The BC₁S₁ population exhibited a continuous variation, typical of quantitative traits, with the survival rate of the BC₁S₁ families ranging from 9% to 94% with a mean of 51%. Two QTL mapping techniques, interval mapping (using MAPMAKER/QTL) and single-marker analysis (using QGENE), were used to identify QTLs. The results of both methods were similar and five QTLs were identified on chromosomes 1 (two QTLs), 3, 5 and 9. Each QTL accounted for between 5.7% and 17.7%, with the combined effects (of all five QTLs) exceeding 46%, of the total phenotypic variation. All QTLs had the positive QTL alleles from the salt-tolerant parent. Across QTLs, the effects were mainly additive in nature. Digenic epistatic interactions were evident among several QTL-linked and QTL-unlinked markers. The overall results indicate that tomato salt tolerance during the vegetative stage could be improved by marker-assisted selection using interspecific variation. Received: 4 January 1999 / Accepted: 4 January 1999