Quantitative trait loci for seed dormancy in rice

Seed dormancy (SD) is controlled by its own complicated genetic factors and environmental factors. SD is an important trait affecting grain yield and quality in cereal crops. A population comprising 240 recombinant inbred lines (RIL) was used for detecting quantitative trait locus (QTL) for SD in rice. To minimize the effect of environment, data for lines for which the optimum temperature during the late ripening stage is either below 20°C or above 30°C were excluded from the analysis, which left 185 lines. In a dynamic germination test of the parents of the population, Minghui 63 showed clear SD and Zhenshan 97 showed none. The seeds of each RIL, harvested 32 days after heading, were divided into two lots: seeds in one lot were sown immediately, without any treatment to break their dormancy, whereas seeds in the other lot were sown after they had been exposed to dry heat (50°C) for 72 h. Composite interval mapping showed the presence of qDGE1, qDGR5a, qDGR5b, and qDGR7 in the first lot whereas only qDGR7 was detected in the second lot––which had been treated to break SD––indicating the strong influence of qDGR7 in controlling SD. A recently cloned Sdr4 is also located in the qDGR7 region. Coincidently, three rice homologues of Arabidopsis SD gene DOG1 were found in qDGE1 and qDGR5b regions where no SD QTL had been reported so far. These results indicate that the QTL found in this study are reliable, and that it would be worthwhile to clone qDGE1 and qDGR5b.     

Quantitative trait loci mapping and stability for low temperature germination ability of rice

A high rate of germination at low temperatures is necessary for economic yields to be maintained. In this paper, the genetic control of low temperature germination ability (LTG) was assessed by the measurement of germination rate (GR), germination rate index (GI) and mean germination time (MGT), and genetically mapped using a set of recombinant inbred lines, derived from a cross between the japonica cultivar 'Asominori' and the indica cultivar 'IR24'. Putative quantitative trait loci (QTL) were validated by testing in two related sets of chromosome segment substitution lines (CSSL). In this genetic background, LTG is under the control of a number of QTL, each of relatively small effect, and is spread over six chromosomes. The most stable of these QTL was for GR, mapping to a segment of chromosome 11 which also carries a QTL for GI. On chromosome 2, qGR-2 not only controlled GR, but also was associated with GI and MGT. Significant differences in LTG were detected between 'Asominori' and some CSSL harbouring qGR-2 or qGR-11 .     

Mapping of quantitative trait loci controlling seed longevity of rice (Oryza sativa L.) after various periods of seed storage

Seed longevity varies considerably in cultivated rice (Oryza sativa L.), but the underlying genetic mechanism of longevity has not been well elucidated. Quantitative trait loci (QTL) that control seed longevity after various periods of seed storage were sought using recombinant inbred lines derived from a combination involving ‘Milyang23’(Indica‐type) and ‘Akihikari’ (Japonica‐type). In all, 12 QTLs for germination and normal seedling growth were detected as indices of seed longevity on chromosome 7 (one region) and chromosome 9 (two regions) in treated seeds that had been stored under laboratory conditions for 1, 2 or 3 years.‘Milyang23’ alleles of all QTLs promoted germination and normal seedling growth after all durations of storage. These QTL regions were detected repeatedly in more than one seed condition. Therefore, we infer that these regions control seed longevity.     

Quantitative trait loci for adventitious and lateral roots in rice

The mass of a root is determined by two underlying morphogenetic factors: (1) the length of the main root axis (root axis length: RAL), and (2) the amount of lateral root development generated by a unit length of the axis (branching index: BI). The mass of a rice adventitious root was partitioned into these two factors at the quantitative trait locus (QTL) level, using ‘Akihikari’ (a lowland cultivar as a recurrent parent) × ‘IRAT 109’ (an upland cultivar) backcross inbred lines. Four QTLs were detected for the dry weight of individual adventitious roots (root dry weight: RDW), which were associated with a QTL for RAL (chromosomes 1 and 9) or a QTL for BI (chromosomes 6 and 11). For BI, an additional QTL was detected on chromosome 1. The absence of co‐located QTLs suggested that RAL and BI are under separate genetic control. Despite its small population size and few replications, this study suggests that the partitioning of root mass into these underlying components could be useful for understanding the complexity involved in the genetic control of root growth.     

Comparison of QTLs for seed germination under non-stress, cold stress and salt stress in tomato

The purpose of this study was to examine whether rate of tomato seed germination under non-stress, cold-stress and salt-stress conditions was under similar genetic control by identifying and comparing quantitative trait loci (QTLs) which affect germination rate under these conditions. A fast-germinating accession (LA722) of the wild tomato species Lycopersicon pimpinellifolium Jusl. and a slow-germinating cultivar (NC84173, maternal and recurrent parent) of tomato (Lycopersicon esculentum Mill.) were hybridized and BC₁ and BC₁S₁ progeny produced. The BC₁ population was used to construct a linkage map with 151 restriction fragment length polymorphism (RFLP) markers. The BC₁S₁ population (consisting of 119 BC₁S₁ families) was evaluated for germination under non-stress (control), cold-stress and salt-stress conditions and the mean time to 50% germination (T50) in each treatment was determined. Germination analyses indicated the presence of significant (P < 0.01) phenotypic correlations between T50 under control and cold stress (r = 0.71), control and salt stress (r = 0.58) and cold stress and salt stress (r = 0.67). The QTL analysis indicated the presence of genetic relationships between germination under these three conditions: a few QTLs were identified which commonly affected germination under both stress- (cold-, salt- or both) and non-stress conditions, and thus were called stress-nonspecific QTLs. A few QTLs were also identified which affected germination only under cold or salt stress and thus were called stress-specific QTLs. However, the stress-nonspecific QTLs generally exhibited larger individual effects and together accounted for a greater portion of the total phenotypic variation under each condition than the stress-specific QTLs. Whether the effects of stress-nonspecific QTLs were due to pleiotropic effects of the same genes, physical linkage of different genes, or a combination of both could not be determined in this study. The results, however, indicate that the rate of tomato seed germination under different stress and nonstress conditions is partly under the same genetic control.     

Quantitative trait loci for stomatal density and size in lowland rice

Genotypic variation in stomatal density and size has been reported but little is known of the genetic mechanisms behind these leaf traits. Using 101 recombinant inbred lines derived from a cross between a tropical japonica, IR69093-41-3-2-2 and an indica variety, IR72, we conducted a field study to determine stomatal density and size and identify quantitative trait loci (QTL) controlling these traits under lowland conditions. Ten QTLs for stomatal density and four QTLs for size were identified across growth stages and leaf surfaces (adaxial and abaxial). The contribution of each QTL to total phenotypic variation ranged from 9.3 to 15.2% for stomatal density and 9.7 to 14.3% for size. The allele from IR72 increased stomatal density and that from IR69093-41-3-2-2 increased size. The expression of the QTLs for stomatal density and size differed by growth stage indicating that these traits might be genetically controlled depending on growth stage or that each QTL had a different function by growth stage. Significant negative genetic correlations between stomatal density and size at both vegetative (r = −0.308**) and heading (r = −0.484**) stages were observed but no common QTL for these traits was detected across growth stages and leaf surfaces. These results indicate that the QTLs for density and size may neither be genetically linked nor pleiotropically controlled and findings can be used as basis for selection at the leaf level on the balance of carbon and water uptake. Further study is needed to fully understand the mechanism underlying the observed genetic association and to elucidate the function of the QTLs involved.     

NaCl胁迫对秦艽种子萌发的影响

研究了不同浓度NaC1溶液对秦艽种子萌发的影响.结果表明:高浓度NaC1对秦艽种子的萌发有明显的抑制作用,种子的发芽率与盐浓度之间呈显著的负相关.低浓度NaC1(≤50mmol/L) 进种子萌发,高浓度的NaC1(≥150mmol/L)抑制种子萌发:种子萌发时盐胁迫的适宜值、临界值、极限值分别是51.14、160.46、204.26mmol/L.     

盐胁迫对海岛棉种子萌发的影响

研究不同浓度盐胁迫对海岛棉种子萌发和幼苗生长的影响,结果表明:两个供试品种新海21号和新海23号均表现为:①低浓度的NaCl(≤25mmol/L)对海岛棉种子发芽抑制作用较小或无影响,而高浓度的NaCl(≥50mmol/L)则表现出强烈的抑制作用;②无论盐浓度高低,都对海岛棉的幼苗生长产生抑制作用,当NaCl≥125mmol/L时,幼苗的根、茎、叶、根冠比和总干重均显著低于对照;③两个供试品种,新海23号较新海21号耐盐。     

Mapping of quantitative trait loci controlling seedling vigor in rice (Oryza sativa L.) under submergence

Submergence-induced suppression of seedling vigor is a serious constraint particularly in the direct seeding rice cultivation system. To identify quantitative trait loci (QTLs) associated with seedling vigor in rice under submergence, a mapping population of 98 Backcross Inbred Lines derived from a cross of Nipponbare/Kasalath//Nipponbare was used. Phenotypic evaluation of seedling vigor under submergence was based on shoot length (SHL), root length (RTL) and shoot fresh weight (SFW) using a test tube bioassay method. Thirty-two putative QTLs were detected among which 7 were for SHL, 11 for RTL and 14 for SFW. Phenotypic evaluation was also made of the parental lines and a set of 54 chromosome segment substitution lines in which Nipponbare segments were substituted for by their homologous Kasalath segments covering the entire rice genome. Two QTLs with more than 10 % contribution to the total phenotypic variance were verified for SHL, and at least one for RTL and six for SFW on chromosomes 1, 3, 4, 6 and 7 at the 1 % significance level. Among these, all but two showed reductions in one, two or all three traits. Our present and previous results suggest that the Nipponbare genome has a potential to improve seedling vigor under submergence and that japonica germplasms can be used to breed for this important trait in indica rice.     

Quantitative trait loci mapping of maize (Zea mays) ear traits under low-phosphorus stress

We constructed an F_2:3 population of 180 individuals from a cross between the maize genotypes 082 (high phosphorus use efficiency) and Ye107 (low phosphorus use efficiency). We used the population to perform quantitative trait loci (QTL) mapping for eight ear traits (ear diameter [ED], ear length [EL], ear weight [EW], ear kernel weight [EKW], row number per ear [ERN], bald tip length [BTL], kernel number per row [RKN] and number of seeds per plant [NSP]) in three low-phosphorus environments. A total of 36 QTL for ear traits were detected in at least one of three single environments and were located on all maize chromosomes except for chromosome 10; the explained phenotypic variation ranged from 5.91% to 12.80%. The QTL JAqEKW5-1, JAqEL3-1, JAqEW1-1, JAqBTL1-1 and JAqNSP5-2 were identified and stably expressed in single-environment and joint-environment analyses. Some novel QTL that have not been reported previously were also detected. Most of the identified QTL had stable effects in all low-phosphorus environments, suggesting that they may be useful for molecular breeding to develop low-phosphorus tolerant maize varieties.     

Quantitative trait loci for whiteness of cooked rice detected in improved rice cultivars in Hokkaido

Improving the eating quality of cooked rice has been one of the most important objectives in rice breeding programs. Eating quality of cooked rice is a complex trait including several components, such as external appearance, taste, aroma, and texture. Therefore, dissection of these components followed by marker-assisted selection of detected QTL(s) may be a useful approach for achieving desirable eating quality in rice breeding. Whiteness of cooked rice (WCR) is an important factor related to the external appearance of cooked rice. WCR is known to be associated with the amylose and protein contents of the endosperm. However, the genetic basis of WCR remains unclear. In this study, we evaluated phenotypic variation in WCR among recently developed rice cultivars from Hokkaido, Japan. Then, we developed doubled haploid lines (DHLs) derived from a cross between two cultivars from Hokkaido, Joiku No. 462 (high WCR) and Jokei06214 (low WCR). Using the DHLs, we detected two QTLs for WCR, qWCR3 and qWCR11, on chromosomes 3 and 11, respectively. We also examined the dosage effect of the two QTLs based on both the categorized segregants in the DHLs and the relationship between the WCR phenotype and inheritance around the QTL regions in cultivars from Hokkaido.     

Quantitative trait loci associated with seed set under high temperature stress at the flowering stage in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

High temperature stress (HTS), an increasingly important problem in rice production, significantly reduces rice yield by reducing seed set percentage (SSP). Breeding rice varieties with tolerance to HTS at the flowering stage is therefore essential for maintaining rice production as the climate continues to warm. In this study, two quantitative trait loci (QTL) underlying tolerance to HTS were identified using the recombinant inbred lines (RILs) derived from a cross between the HTS-tolerant rice cultivar 996 and the sensitive cultivar 4628. SSP was used as the heat-tolerance indicator for the lines, which were subjected to HTS at the flowering stage in both field and growth chamber experiments. Two major QTL that affected SSP in both conditions were detected in the interval between RM5687 and RM471 on chromosome 4, and between RM6132 and RM6100 on chromosome 10. The QTL located on chromosome 4 explained 21.3% in field and 25.8% in growth chamber of the total phenotypic variation in SSP, and increased the SSP of plants subjected to HTS by 9.1% in field and by 9.3% in growth chamber. The second QTL located on chromosome 10 explained 11.5% in field and 11.6% in growth chamber of the total phenotypic variation in SSP, and increased the SSP of plants subjected to HTS by 7.2% in field and 7.0% in growth chamber. The positive additive effects of the two QTL were derived from the 996 alleles. The two major QTL identified in this study could be useful for further fine mapping and cloning of these genes and for molecular marker-aided breeding of heat-tolerant rice cultivars.     

Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping

Plant breeding programs aim to develop cultivars with high adaptability to the specific conditions in a local region. As a result, unique genes and gene combinations have been accumulated in local elite breeding populations during the long history of plant breeding. Genetic analyses on such genes and combinations may be useful for developing new cultivars with more-desirable agronomic traits. Here, we attempted to detect quantitative trait loci (QTL) for rice blast resistance (BR) using a local breeding rice population from Hokkaido, Japan. Using genotyping data on single nucleotide polymorphisms and simple sequence repeat markers distributed throughout the whole genomic region, we detected genetic regions associated with phenotypic variation in BR by a genome-wide association mapping study (GWAS). An additional association analysis using other breeding cultivars verified the effect and inheritance of the associated region. Furthermore, the existence of a gene for BR in the associated region was confirmed by QTL mapping. The results from these studies enabled us to estimate potential of the Hokkaido rice population as a gene pool for improving BR. The results of this study could be useful for developing novel cultivars with vigorous BR in rice breeding programs.     

Quantitative trait loci for phytate in rice grain and their relationship with grain micronutrient content

Phytate (inositol-hexa-phosphate) has an important role in plants but it also may have anti-nutritional properties in animals and humans. While there is debate within the plant breeding and nutrition communities regarding an optimum level in grain, there appears to be little information at the molecular level for the genetics of this trait, and its association with important trace elements, in particular, Fe and Zn. In this preliminary study, quantitative trait loci (QTL) for grain phytates, Zn and Fe in glasshouse-grown rice lines from an IR64 × Azucena doubled haploid population were identified. Correlations between phytate and essential nutrients were also studied. Transgressive segregation was found for most traits. Phytate and total P concentrations had one QTL in common located on chromosome five with the (high concentration) allele contributed from Azucena. There were significant positive correlations between phytate and inorganic phosphorus (P), total P, Fe, Zn, Cu and Mn concentrations for both grain concentration and content. However, the QTLs of phytate were not located on the same chromosomal regions as those found for Fe, Zn and Mn, suggesting that they were genetically different and thus using molecular markers in breeding and selection would modify the phytate level without affecting grain micronutrient density.     

Quantitative trait loci for agronomic traits in soybean

There continues to be improvement in seed yields of soybean by conventional breeding, but molecular techniques may provide faster genetic gains. The objective of this study was to identify quantitative trait loci (QTL) associated with the agronomic traits seed yield, lodging, plant height, seed filling period and plant maturity in soybean. To achieve this objective, 101 F₆‐derived recombinant inbred lines (RIL) from a population developed from a cross of N87‐984‐16 × TN93‐99 were used. Experiments were conducted in six environments during 2002–2003. Heritability estimates on an entry mean basis from data combined across environments ranged from 0.12 to 0.65 for seed yield and seed filling period, respectively. Composite interval mapping detected one QTL for yield (near Satt076), two for lodging (near Satt225 and Satt593) and four for maturity (near Satt263, Satt292, Satt293 and Satt591) in this population. Additional environmentally sensitive QTL for these traits, and for seed filling period and plant height are also reported. The QTL associated with agronomic traits that we report and the recently released germplasm (PI 636460) from this population may be useful in soybean breeding programmes.     

Quantitative trait loci for grain-quality traits across a rice F2 population and backcross inbred lines

Improving grain-quality is an important goal in rice breeding programs. One vital step is to find major quantitative trait loci (QTLs) for quality related traits and then investigate the relationships among them. We crossed ‘N22’, an indica variety with good appearance but low grain weight, to a japonica variety, ‘Nanjing35’, with superior grain yield but poor appearance. This enabled us to construct an F₂ population and a set of backcross inbred lines (BILs) for QTL-mapping for the traits related grain appearance. In all, 37 QTLs were identified for grain length (GL), grain width (GW), grain thickness (GT), thousand-grain weight (TGW), and the percentage of grains with chalkiness (PGWC). Of these, 17 QTLs detected from 184 plants in the F₂ population explained 4.97–27.26 % of the phenotypic variance, another 20 QTLs were identified using BILs from 2009 to 2010. Quantitative trait loci for major effects were detected in different populations and across years. A new QTL hot spot (marker interval RM504–RM520) was found on Chromosome 3, which harbored QTLs for GL, GW, GT, and TGW. Among our five examined traits, grain shape was significantly correlated with TGW and PGWC. The PGWC values of two heavier grains BILs, L93, and L145 are much lower than Nanjiing35, the analysis of genotype showed that this greater weight may due to the locus for GL occurring within RM504–RM520 on Chromosome 3. Therefore, those two lines will allow us to develop a long-grain high-yield rice variety with less chalkiness.     

盐胁迫对菜心种子发芽及幼苗生长的影响

对菜心种子在NaCl、MgS04、CaCl2 3种不同盐溶液浓度的胁迫下进行种子发芽研究,观察其发芽率,称量幼苗鲜重.结果表明,在菜心种子发芽期,其萌芽及生长受盐成分及浓度影响较大;团棵期幼苗抗盐能力为0.6%,说明菜心抗中等盐碱.     

盐胁迫对4种禾本科牧草种子萌发和幼苗生长的影响

通过NaCl溶液(0、1.5、3.0、6.0、9.0g/L)处理4种禾本科牧草种子,测定了种子萌发和幼苗生长有关指标。结果表明：美洲狼尾草较耐盐,在9.0g/L盐溶液处理下比其它品种维持了高的发芽率、发芽指数、活力指数,并且其相对值高,以及较高的相对苗长和根长,盐处理显著提高几种牧草幼苗质膜相对透性,总体上降低胚乳的利用速度和利用效率。