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.     

Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice

Seed vigor is an index of seed quality that is used to describe the rapid and uniform germination and the establishment of strong seedlings in any environmental conditions.Strong seed vigor in low-temperature germination conditions is particularly important in direct-sowing rice production systems. However, seed vigor has not been selected as an important breeding trait in traditional breeding programs due to its quantitative inherence. In this study, we identified and mapped eight quantitative trait loci(QTLs) for seed vigor by using a recombinant inbred population from a cross between rice(Oryza sativa L. ssp. indica) cultivars ZS97 and MH63.Conditional QTL analysis identified qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-11 influenced seedling establishment and that qSV-5a, qSV-5c, and qSV-8 influenced only germination. Of these,qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-8 were low-temperature-specific QTLs. Two major-effective QTLs, qSV-1, and qSV-5c were narrowed down to 1.13-Mbp and 400-kbp genomic regions, respectively. The results provide tightly linked DNA markers for the marker-assistant pyramiding of multiple positive alleles for increased seed vigor in both normal and low-temperature germination environments.     

Identification of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populations

Plant growth and development are tightly linked to primary metabolism and are subject to natural variation. In order to obtain an insight into the genetic factors controlling biomass and primary metabolism and to determine their relationships, two Arabidopsis thaliana populations [429 recombinant inbred lines (RIL) and 97 introgression lines (IL), derived from accessions Col-0 and C24] were analyzed with respect to biomass and metabolic composition using a mass spectrometry-based metabolic profiling approach. Six and 157 quantitative trait loci (QTL) were identified for biomass and metabolic content, respectively. Two biomass QTL coincide with significantly more metabolic QTL (mQTL) than statistically expected, supporting the notion that the metabolic profile and biomass accumulation of a plant are linked. On the same basis, three out the six biomass QTL can be simulated purely on the basis of metabolic composition. QTL based on analysis of the introgression lines were in substantial agreement with the RIL-based results: five of six biomass QTL and 55% of the mQTL found in the RIL population were also found in the IL population at a significance level of P  ≤ 0.05, with >80% agreement on the allele effects. Some of the differences could be attributed to epistatic interactions. Depending on the search conditions, metabolic pathway-derived candidate genes were found for 24–67% of all tested mQTL in the database AraCyc 3.5. This dataset thus provides a comprehensive basis for the detection of functionally relevant variation in known genes with metabolic function and for identification of genes with hitherto unknown roles in the control of metabolism.     

RFLP mapping of QTLs conferring cold tolerance during seed germination in an interspecific cross of tomato

Most cultivars of tomato, Lycopersicon esculentum, are sensitive to low (chilling) temperatures (0–15 °C) during seed germination; however, genetic sources of cold (chilling) tolerance have been identified within the related wild species. The purpose of this study was to identify quantitative trait loci (QTLs) that contribute to cold tolerance during germination in tomato using a backcross population of an interspecific cross between a cold-sensitive tomato line (NC84173, recurrent parent) and a L. pimpinellifolium accession (LA722) that germinates rapidly under low temperatures. A total of 119 BC1 individuals were genotyped for 151 restriction fragment length polymorphism (RFLP) markers and a genetic linkage map was constructed. The parental lines and 119 BC1S1 families (self-pollinated progeny of the BC1 individuals) were evaluated for germination at a low temperature (11±0.5 °C). Germination was scored visually as radicle protrusion at 8 h intervals for 28 consecutive days. Germination response was analyzed by the survival analysis and the times to 25, 50 and 75% germination were calculated. In addition, a germination index (GI) was calculated as the weighted mean of the time from imbibition to germination for each family/line. Two QTL mapping techniques, interval mapping (using MAPMAKER/QTL) and single-point analysis (using QGENE), were used to identify QTLs. The results of both methods were similar and two chromosomal locations (3–5 putative QTLs) with significant effects on low temperature germination were identified. The L. pimpinellifolium accession had favorable QTL alleles on chromosomes 1 and NC84173 had favorable QTL alleles on chromosome 4. The percentage of phenotypic variation explained (PVE) by individual QTLs ranged from 11.9% to 33.4%. Multilocus analysis indicated that the cumulative action of all significant QTLs accounted for 43.8% of the total phenotypic variance. Digenic epistatic interactions were evident between two of the QTL-linked markers and two unlinked markers. Transgressive phenotypes were observed in the direction of cold sensitivity. The results indicate that low temperature germination of tomato seed can be improved by marker-assisted selection.     

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.     

Effect of lanthanum on aged seed germination of rice

Attempts were made to promote germination of natural aged rice seeds by treating them with lanthanum nitrate. In tests to measure the germination rate, germination index, and vigor index of natural aged rice seeds were found to be significantly increased by lanthanum. It is treating aged rice seed with lanthanum nitrate that enhanced the respiratory rate and activities of superoxide dismutase, catalase, and peroxidase, and decreased superoxide and malondidehyde contents, and therefore reduced plasma membrane permeability. It suggests that lanthanum may be used to pretreat seed before sowing.     

中国杂草稻种群的发芽期耐冷性研究

以中国75个杂草稻种群及其对应采样田的水稻品种为试验材料,研究了不同处理(破除休眠与不破除休眠、常温25℃与低温15℃、7 d测定和14 d测定)对种子发芽率的影响。结果表明,杂草稻的发芽率与对应采样点水稻品种的发芽率呈现极显著相关性。杂草稻破除休眠处理的发芽率显著或极显著高于不破除休眠处理。破除休眠与不破除休眠下,15℃处理的杂草稻种子发芽率均显著高于对应采样田的水稻品种,证明杂草稻相对于采样田水稻品种具有更强的耐冷性,可能进化出了新的耐冷性机制。25℃处理下杂草稻和对应水稻品种的发芽率均与纬度呈显著或极显著负相关,表明休眠性有随着纬度的降低而减弱的趋势。     

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.     

Identification of heterotic metabolite QTL in Arabidopsis thaliana RIL and IL populations

Two mapping populations of a cross between the Arabidopsis thaliana accessions Col-0 and C24 were cultivated and analyzed with respect to the levels of 181 metabolites to elucidate the biological phenomenon of heterosis at the metabolic level. The relative mid-parent heterosis in the F₁ hybrids was <20% for most metabolic traits. The first mapping population consisting of 369 recombinant inbred lines (RILs) and their test cross progeny with both parents allowed us to determine the position and effect of 147 quantitative trait loci (QTL) for metabolite absolute mid-parent heterosis (aMPH). Furthermore, we identified 153 and 83 QTL for augmented additive (Z₁) and dominance effects (Z₂), respectively. We identified putative candidate genes for these QTL using the aracyc database ( http://www.arabidopsis.org/biocyc ), and calculated the average degree of dominance, which was within the dominance and over-dominance range for most metabolites. Analyzing a second population of 41 introgression lines (ILs) and their test crosses with the recurrent parent, we identified 634 significant differences in metabolite levels. Nine per cent of these effects were classified as over-dominant, according to the mode of inheritance. A comparison of both approaches suggested epistasis as a major contributor to metabolite heterosis in Arabidopsis. A linear combination of metabolite levels was shown to significantly correlate with biomass heterosis ( r  = 0.62).     

水稻单片段代换系代换片段的QTL鉴定

利用以台中65为受体、窄叶青和低脚乌尖为供体培育的10个水稻单片段代换系为材料,对代换片段上21个重要农艺性状的QTL进行了鉴定。10个代换片段的总长度为230．00cM,占水稻基因组总长度的12．62％。通过t测验比较单片段代换系与受体亲本的表型差异,以P≤0．001为阈值,在10个代换片段上共鉴定出17个性状的57个QTL,平均每个性状鉴定出3．35个,这些QTL分布于第1、3、5、7、8、10和12染色体上。57个QTL的加性效应百分率在1．10％～89．73％之间,其中15个QTL的加性效应百分率大于10％,30个QTL在3％-10％之间,12个QTL小于3％。     

Dissection of genetic overlap of salt tolerance QTLs at the seedling and tillering stages using backcross introgression lines in rice

QTLs for salt-tolerance(ST)related traits at the seedling and tillering stages were identified using 99 BC2F8 introgression lines(IL)derived from a cross between IR64(indica)as a recurrent parent and Binam(japonica)from Iran as the donor parent.Thirteen QTLs affecting survival days of seedlings(SDS), score of salt toxicity of leaves(SST),shoot K concentration(SKC)and shoot Na concentration(SNC) at the seedling stage and 22 QTLs underlying fresh weight of shoots(FW),tiller number per plant(TN) and plant height(PH)at the tillering stage were identified.Most QTLs detected at the tillering stage showed obvious differential expression to salt stress and were classified into three types based on their differential behaviors.Type I included 11 QTLs which were expressed only under the non-stress condition.Type II included five QTLs expressed in the control and the salt stress conditions,and three of them(QPh5,QPh8 and QTn9)had similar quantity and the same direction of gene effect,suggesting their expression was less influenced by salt stress.Type III included six QTLs which were detectable only under salt stress,suggesting that these QTLs were apparently induced by the stress.Thirteen QTLs affecting trait difference or trait stability of ILs between the stress and non-stress conditions were identified and the Binam alleles at all loci except QPh4,QTn2 and QFw2a decreased trait difference.The three QTLs less influenced by the stress and 13 QTLs affecting trait stability were considered as ST QTLs which contributed to ST.Comparing the distribution of QTLs detected at the seedling and tillering stages,most(69%)of them were genetically independent.Only four were the same or adjacent regions on chromosomes 1,2,8 and 11 harboring ST QTLs detected at the two stages,suggesting that partial genetic overlap of ST across the two stages occurs.It is likely,therefore,to develop ST rice variety for both stages by pyramiding of ST QTLs of different stages or selection against the overlapping QTLs between the two stages via marker-assisted selection(MAS).     

水稻叶片性状和根系活力的QTL定位

应用由247个株系组成的珍汕97B/密阳46重组自交系(RIL)群体及其分子标记连锁图谱,检测控制剑叶、倒二叶、倒三叶的5个形态性状和控制根系伤流量性状的数量性状座位(QTL)。在9个标记区间检测到控制叶片形态性状的24个QTL,LOD值为2．9～11．8,单个QTL的表型变异贡献率为4．0％～32．5％;分别检测到56对和4对控制叶片形态和根系活力的上位性互作,绝大多数互作发生在2个不表现加性效应的座位之间。与该群体产量性状QTL的研究结果相比较,发现控制叶片性状和根系活力的QTL与产量性状QTL往往处于相似的染色体区间。     

Quantitative genetic analysis of seed vigour and pre-emergence seedling growth traits in Brassica oleracea

The ability of seeds to germinate and establish seedlings in a predictable manner under a range of conditions has a direct contribution to the economic success of commercial crops, and should therefore be considered in crop improvement. We measured traits associated with seed vigour and pre-emergence seedling growth in a segregating population of 105 doubled haploid Brassica oleracea lines. The germination traits measured were: mean germination times for unstressed germination; germination under water stress or germination after a heat treatment; and conductivity of seed leachate. The seedling growth traits measured were: seed weight; seedling growth rate; and seedling size at the end of the exponential growth phase. There were some correlations, notably among germination traits, and between seed weight and pre-emergence seedling growth. Heritability of the various traits was typically in the 10–15% range, with heritability of conductivity and mean germination time under water stress 25 and 24% respectively. Collectively the results indicate that germination and pre-emergence seedling growth are under separate genetic control. Quantitative trait loci analyses were carried out on all measurements and revealed significant loci on linkage groups O1, O3, O6, O7 and O9. We suggest that genes at these loci are important in determining predictable seed germination and seedling establishment in practice.     

Identification of quantitative trait loci controlling rice mature seed culturability using chromosomal segment substitution lines

The genetic transformation efficiency of a rice variety is largely determined by its tissue culturability. Establishment of a highly efficient tissue-culture system has greatly accelerated the wide spread application of transgenic japonica varieties. However, such process for indica rice was hampered because this type of variety is recalcitrant to in vitro culture. This study aimed to map the quantitative trait loci (QTLs) for mature seed culturability using a chromosomal segment substitution lines (CSSL) population derived from a cross between an indica variety “Zhenshan 97B” and a japonica variety “Nipponbare”. The CSSLs consist of 139 lines each containing a single or a few introgression segments, and together covering the whole “Nipponbare” genome. Every CSSL was tested by culturing on the two medium systems developed for the respective indica and japonica parental varieties. The performance of culturability was evaluated by four indices: frequency of callus induction (CIF), callus subculture capability (CSC), frequency of plant regeneration (PRF) and the mean plantlet number per regenerated callus (MNR). All four traits displayed continuous variation among the CSSLs. With the culture system for japonica rice, three CIF QTLs, three CSC QTLs, three PRF QTLs and three MNR QTLs were detected. With the culture system for indica variety, six CIF QTLs, two CSC QTLs, three PRF QTLs and six MNR QTLs were identified, and these QTLs distributed on nine rice chromosomes. Two QTLs of CIF and two QTLs of MNR were detected in both the japonica and indica rice culture system. The correlation coefficients of all the four traits varied depending on the culture systems. These results provide the possibilities of enhancing the culturability of indica rice by marker-assisted breeding with those desirable alleles from the japonica. Lina Zhao and Hongju Zhou have contributed equally to this work.     

Epistasis plays an important role as genetic basis of heterosis in rice

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QTLs for nitrate induced elongation and initiation of lateral roots in rice (Oryza sativa L.)

To investigate the genetic background of nitrate-induced elongation and initiation of lateral roots in rice (Oryza sativa L.), a doubled haploid (DH) population, derived from a cross between IR64 and Azucena, which showed different responses to local supplied NO₃ ^– in lateral root elongation and initiation, was used in an agar culture experiment with three separated layers. The second agar layer was supplied with 3 mM NO₃ ^– or without NO₃ ^– as two treatments. Average lateral root length, lateral root number and surface area of lateral roots in the second agar layers with and without nitrate, respectively, were measured. The ratio of the parameters from the two treatments were calculated as derived parameters. Seven putative Quantitative trait loci (QTLs) for the 6 lateral root traits in nitrate-deficient and nitrate-supplied layers were detected. These QTLs individually explained about 9% to 15% of the total phenotypic variations in the traits. Identical QTLs for root traits from other reports with QTLs detected in this case were found, which suggests that the genetic factors responsive to local supplied NO₃ ^– is involved in root growth and development     

Role of seed germination in adaptation and reproductive isolation in Arabidopsis lyrata

Seed germination is an important developmental and life history stage. Yet, the evolutionary impact of germination has mainly been studied in the context of dormancy, or for its role in reproductive isolation between species. Here, we aim to examine multiple consequences of genetic divergence on germination traits between two Arabidopsis lyrata subspecies: ssp. petraea (Eurasia) and ssp. lyrata (North America). Postdormancy germination time, a potentially adaptive trait, showed differentiation between the populations, and quantitative trait loci (QTL) mapping revealed that the trait variation is mainly controlled by two antagonistic loci. These QTL areas contain several candidate genes with known function in postdormancy germination in A. thaliana. The sequence variation of three genes was consistent with differential selection, and they also included fixed nonsynonymous substitutions with potential to account for the phenotypic differentiation. We further show that the divergence between the subspecies has led to a slight but significant reduction in hybrid germination proportions, indicating incipient reproductive isolation. Comparison of reciprocal F₁ and F₂ progenies suggests that Bateson–Dobzhansky–Muller incompatibilities likely act through uniparentally inherited factors. Examination of genomewide transmission ratio distortion further revealed that cytonuclear interactions cause substantial pregermination inviability in the hybrids. These results confirm that seed germination has adaptive potential beyond the dormancy stage and that hybrid seed inviability can be one of the first reproductive barriers to arise during divergence.     

不同居群准噶尔无叶豆果实和种子特性及种子萌发差异

研究准噶尔无叶豆(Eremosparton songoricum) 6个居群间果实和种子特性及种子萌发差异, 以揭示异质生境下准噶尔无叶豆果实和种子的生态适应机制。结果显示: 居群间准噶尔无叶豆的植株距离(F = 2.34, p = 0.03)和植株冠幅(F = 8.49, p < 0.01)存在显著差异, 沙漠北缘E、F居群和沙漠腹地C居群(受人类干扰剧烈)的植株距离和植株冠幅高于沙漠腹地A、B、D居群; 居群间准噶尔无叶豆果实和种子的长度、宽度、厚度、重量存在显著差异, 居群E、F和C的大部分参数显著高于其他沙漠腹地居群; 居群间果实多子性(F = 6.96, p < 0.01)也存在显著差异, 居群C的果实多子性最高((32.50 ± 4.79)%); 萌发结果表明, 居群间新鲜的成熟种子萌发不存在显著差异, 且萌发率都低于15%; 所有居群的大部分种子都存在物理性休眠现象, 人为划破种皮能显著提高种子萌发率, 但在低温(15/5 ℃)条件下, 所有居群的种子萌发率都较低, 说明低温抑制了种子萌发; 经人为划破种皮解除物理休眠后, 种子的休眠没有完全释放, 居群C、E和F (大种子居群)的种子萌发率显著高于居群A、B和D (小种子居群) (F = 30.77, p < 0.01), 说明准噶尔无叶豆种子不仅存在物理性休眠现象, 也可能存在生理休眠现象。不同程度的种子复合休眠可能是准噶尔无叶豆不同居群适应古尔班通古特沙漠的重要生存策略。     

Identification of QTLs Involved in the Development of Amygdala Kindling in the Rat

Amygdala kindling is useful for modeling human epilepsy development. It has been known that genetic factors are involved in the development of amygdala kindling. The purpose of this study was to identify the loci that are responsible for the development of amygdala kindling. To achieve this, rat strains from a LEXF/FXLE recombinant inbred (RI) strain panel were used. The phenotypes of amygdala kindling-related parameters for seven RI strains and parental LE/Stm and F344/Stm strains were determined. They included the afterdischarge threshold (ADT), the afterdischarge duration (ADD), and the kindling rate, an incidence of development of kindling. Quantitative trait loci (QTL) analysis was performed to identify linkage relationships between these phenotypes and 1,033 SNP markers. Although no significant differences in pre-kindling ADT and ADD were observed, a significant difference in the kindling rate was found for the LEXF/FXLE RI strain. Two QTLs for the amygdala kindling rate (Agkr1 and Agkr2) were identified on rat chromosome 2. These findings clearly prove the existence of genetic influences that are involved in kindling development and suggest that substantial genetic components contribute to the progression of partial seizures into generalized seizures.