Detection of loci controlling seed dormancy on group 4 chromosomes of wheat and comparative mapping with rice and barley genomes

Three quantitative trait loci (QTLs) controlling seed dormancy were detected on group 4 chromosomes of wheat (Triticum aestivum L.) using 119 doubled haploid lines (DHLs) derived from a cross between AC Domain and Haruyutaka. A major QTL, designated QPhs.ocs-4A.1, was identified within the marker interval between Xcdo795 and Xpsr115 in the proximal region of the long arm of chromosome 4A. Two minor QTLs, QPhs.ocs-4B.2 on 4B and QPhs.ocs-4D.2 on 4D, were flanked by common markers, Xbcd1431.1 and Xbcd1431.2 in the terminal region of the long arms, suggesting a homoeologous relationship. These three QTLs explained more than 80% of the total phenotypic variance in seed dormancy of DHLs grown in the field and under glasshouse conditions. The AC Domain alleles at the three QTLs contributed to increasing seed dormancy. Comparative maps across wheat, barley and rice demonstrated the possibility of a homoeologous relationship between QPhs.ocs-4A.1 and the barley gene SD4, while no significant effects of the chromosome regions of wheat and barley orthologous to rice chromosome 3 region carrying a major seed dormancy QTL were detected. Received: 5 June 2000 / Accepted: 31 August 2000     

Genetic and QTL analyses of seed dormancy and preharvest sprouting resistance in the wheat germplasm CN10955

The inheritance and genetic linkage analysis for seed dormancy and preharvest sprouting (PHS) resistance were carried out in an F₈ recombinant inbred lines (RILs) derived from the cross between “CN19055” (white-grained, PHS-resistant) with locally adapted Australian cultivar “Annuello” (white-grained, PHS-susceptible). Seed dormancy was assessed as germination index (GI7) while assessment for preharvest sprouting resistance was based on whole head assay (sprouting index, SI) and visibly sprouted seeds (VI). Segregation analysis of the F₂, F₃ data from the glasshouse and the RIL population in 2004 and 2005 field data sets indicated that seed dormancy and PHS resistance in CN19055 is controlled by at least two genes. Heritabilities for GI7 and VI were high and moderate for SI. The most accurate method for assessing PHS resistance was achieved using VI and GI7 while SI exhibited large genotype by environment interaction. Two quantitative trait loci (QTLs) QPhs.dpivic.4A.1 and QPhs.dpivic.4A.2 were identified. On pooled data across four environments, the major QTL, QPhs.dpivic.4A.2, explained 45% of phenotypic variation for GI7, 43% for VI and 20% for SI, respectively. On the other hand, QPhs.dpivic.4A.1 which accounted for 31% of the phenotypic variation in GI7 in 2004 Horsham field trial, was not stable across environments. Physical mapping of two SSR markers, Xgwm937 and Xgwm894 linked to the major QTL for PHS resistance, using Chinese Spring deletions lines for chromosome 4AS and 4AL revealed that the markers were located in the deletion bins 4AL-12 and 4AL-13. The newly identified SSR markers (Xgwm937/Xgwm894) showed strong association with seed dormancy and PHS resistance in a range of wheat lines reputed to possess PHS resistance. The results suggest that Xgwm937/Xgwm894 could be used in marker-assisted selection (MAS) for incorporating preharvest sprouting resistance into elite wheat cultivars susceptible to PHS.     

Identification of eight chromosomes and a microsatellite marker on 1AS associated with QTL for grain weight in bread wheat

The present study in bread wheat was undertaken, firstly, to identify chromosomes carrying QTLs controlling 1000 grain weight (GW) and, secondly, to develop molecular marker(s) linked with this trait. Using the genotype Rye Selection111 (RS111), we carried out a monosomic analysis that suggested that 8 chromosomes (1A, 1D, 2B, 4B, 5B, 6B, 7A and 7D) carried QTLs controlling GW, with only 3 of these (1A, 2B, 7A) carrying alleles for high GW. To tag the QTLs present on these chromosomes, we crossed the genotype RS111 with high GW (56.83 g) with the genotype Chinese Spring (CS) with low GW (23.74 g) and obtained 100 RILs. These RILs showed normal distribution for GW. The parental genotypes were analysed with as many as 346 STMS primer pairs for detection of polymorphism. Of these, 267 primer pairs gave scorable amplification products, 63 of which detected polymorphism between the parents. Using each of these 63 primer pairs, we carried out bulked segregant analysis on RILs representing two extremes of the distribution. One primer pair (WMC333) showed an association of the marker locus Xwmc333 with grain weight. This was confirmed through selective genotyping, and the co-segregation data on molecular marker locus Xwmc333 and GW were analysed following a single marker linear regression approach. Significant regression suggested linkage between Xwmc333 and a QTL for GW. The results showed that the above QTL accounted for 15.09% of the variation for GW between the parents. The marker has been located on chromosome arm 1AS, and QTL was designated QGw1.ccsu-1A. Received: 15 September 1999 / Accepted: 9 November 1999     

Genetic basis of pre-harvest sprouting tolerance using single-locus and two-locus QTL analyses in bread wheat

Quantitative trait loci (QTL) analysis for pre-harvest sprouting tolerance (PHST) in bread wheat was conducted following single-locus and two-locus analyses, using data on a set of 110 recombinant inbred lines (RILs) of the International Triticeae Mapping Initiative population grown in four different environments. Single-locus analysis following composite interval mapping (CIM) resolved a total of five QTLs with one to four QTLs in each of the four individual environments. Four of these five QTLs were also detected following two-locus analysis, which resolved a total of 14 QTLs including 8 main effect QTLs (M-QTLs), 8 epistatic QTLs (E-QTLs) and 5 QTLs involved in QTL × environment (QE) or QTL × QTL × environment (QQE) interactions, some of these QTLs being common. The analysis revealed that a major fraction (76.68%) of the total phenotypic variation explained for PHST is due to M-QTLs (47.95%) and E-QTLs (28.73%), and that only a very small fraction of variation (3.24%) is due to QE and QQE interactions. Thus, more than three-quarters of the genetic variation for PHST is fixable and would contribute directly to gains under selection. Two QTLs that were detected in more than one environment and at LOD scores above the threshold values were located on 3BL and 3DL presumably in the vicinity of the dormancy gene TaVp1. Another QTL was found to be located on 3B, perhaps in close proximity to the R gene for red grain colour. However, these associations of QTLs for PHST with genes for dormancy and grain colour are only suggestive. The results obtained in the present study suggest that PHST is a complex trait controlled by large number of QTLs, some of them interacting among themselves or with the environment. These QTLs can be brought together through marker-aided selection, leading to enhanced PHST.     

Mapping diploid wheat homologues of <Emphasis Type="Italic">Arabidopsis</Emphasis> seed ABA signaling genes and QTLs for seed dormancy

Abscisic acid (ABA) sensitivity in embryos is one of the key factors in the seed dormancy of wheat. Many ABA signaling genes have been isolated in Arabidopsis, while only a few wheat homologues have been identified. In the present study, diploid wheat homologues to Arabidopsis ABA signaling genes were identified by in silico analysis, and mapped them using a population of diploid wheat recombinant inbred lines derived from a cross between Triticum monococcum (Tm) and T. boeoticum (Tb). Four diploid wheat homologues, TmVP1, TmABF, TmABI8 and TmERA1 were located on chromosome 3A^m and TmERA3 was on the centromere region of chromosome 5A^m. In two consecutive year trials, one major QTL on the long arm of 5A^m, two minor QTLs on the long arm of 3A^m and one minor QTL on the long arm of 4A^m were detected. The 5A^m QTL explained 20–27% of the phenotypic variations and the other three QTLs each accounted for approximately 10% of the phenotypic variations. Map positions of the loci of TmABF and TmABI8 matched the LOD peaks of the two QTLs on 3A^m, indicating that these two homologues are possible candidate genes for seed dormancy QTLs. Moreover, we have found two SNPs result in amino acid substitutions in TmABF between Tb and Tm. Comparison of the marker positions of QTLs for seed dormancy of barley revealed that the largest QTL on 5A^m may be orthologous to the barley seed dormancy QTL, SD1, whereas there seems no orthologous QTL to the corresponding barley SD2 locus. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Mapping quantitative trait loci controlling seed dormancy and heading date in rice, Oryza sativa L., using backcross inbred lines

 To detect quantitative trait loci (QTLs) controlling seed dormancy, 98 BC₁F₅ lines (backcross inbred lines) derived from a backcross of Nipponbare (japonica)/Kasalath (indica)//Nipponbare were analyzed genetically. We used 245 RFLP markers to construct a framework linkage map. Five putative QTLs affecting seed dormancy were detected on chromosomes 3, 5, 7 (two regions) and 8, respectively. Phenotypic variations explained by each QTL ranged from 6.7% to 22.5% and the five putative QTLs explained about 48% of the total phenotypic variation in the BC₁F₅ lines. Except for those of the QTLs on chromosome 8, the Nipponbare alleles increased the germination rate. Five putative QTLs controlling heading date were detected on chromosomes 2, 3, 4, 6 and 7, respectively. The phenotypic variation explained by each QTL for heading date ranged from 5.7% to 23.4% and the five putative QTLs explained about 52% of the total phenotypic variation. The Nipponbare alleles increased the number of days to heading, except for those of two QTLs on chromosomes 2 and 3. The map location of a putative QTL for heading date coincided with that of a major QTL for seed dormancy on chromosome 3, although two major heading-date QTLs did not coincide with any seed dormancy QTLs detected in this study. Received: 10 October 1997 / Accepted: 12 January 1998     

Comparative genetic analysis of a wheat seed dormancy QTL with rice and <Emphasis Type="Italic">Brachypodium</Emphasis> identifies candidate genes for ABA perception and calcium signaling

Wheat preharvest sprouting (PHS) occurs when seed germinates on the plant before harvest resulting in reduced grain quality. In wheat, PHS susceptibility is correlated with low levels of seed dormancy. A previous mapping of quantitative trait loci (QTL) revealed a major PHS/seed dormancy QTL, QPhs.cnl-2B.1, located on wheat chromosome 2B. A comparative genetic study with the related grass species rice (Oryza sativa L.) and Brachypodium distachyon at the homologous region to the QPhs.cnl-2B.1 interval was used to identify the candidate genes for marker development and subsequent fine mapping. Expressed sequence tags and a comparative mapping were used to design 278 primer pairs, of which 22 produced polymorphic amplicons that mapped to the group 2 chromosomes. Fourteen mapped to chromosome 2B, and ten were located in the QTL interval. A comparative analysis revealed good macrocollinearity between the PHS interval and 3 million base pair (mb) region on rice chromosomes 7 and 3, and a 2.7-mb region on Brachypodium Bd1. The comparative intervals in rice were found to contain three previously identified rice seed dormancy QTL. Further analyses of the interval in rice identified genes that are known to play a role in seed dormancy, including a homologue for the putative Arabidopsis ABA receptor ABAR/GUN5. Additional candidate genes involved in calcium signaling were identified and were placed in a functional protein association network that includes additional proteins critical for ABA signaling and germination. This study provides promising candidate genes for seed dormancy in both wheat and rice as well as excellent molecular markers for further comparative and fine mapping.     

Fine mapping of a preharvest sprouting QTL interval on chromosome 2B in white wheat

Key message

Fine mapping by recombinant backcross populations revealed that a preharvest sprouting QTL on 2B contained two QTLs linked in coupling with different effects on the phenotype.

Abstract

Wheat preharvest sprouting (PHS) occurs when grain germinates on the plant before harvest, resulting in reduced grain quality. Previous mapping of quantitative trait locus (QTL) revealed a major PHS QTL, QPhs.cnl-2B.1, located on chromosome 2B significant in 16 environments that explained from 5 to 31 % of the phenotypic variation. The objective of this project was to fine map the QPhs.cnl-2B.1 interval. Fine mapping was carried out in recombinant backcross populations (BC₁F₄ and BC₁F₅) that were developed by backcrossing selected doubled haploids to a recurrent parent and self-pollinating the BC₁F₄ and BC₁F₅ generations. In each generation, three markers in the QPhs.cnl-2B.1 interval were used to screen for recombinants. Fine mapping revealed that the QPhs.cnl-2B.1 interval contained two PHS QTLs linked in coupling. The distal PHS QTL, located between Wmc453c and Barc55, contributed 8 % of the phenotypic variation and also co-located with a major seed dormancy QTL determined by germination index. The proximal PHS QTL, between Wmc474 and CNL415-rCDPK, contributed 16 % of the variation. Several candidate genes including Mg-chelatase H subunit family protein, GTP-binding protein and calmodulin/Ca²⁺-dependent protein kinase were linked to the PHS QTL. Although many recombinant lines were identified, the lack of polymorphism for markers in the QTL interval prevented the localization of the recombination breakpoints and identification of the gene underlying the phenotype.     

Identification of genetic loci affecting amylose content and agronomic traits on chromosome 4A of wheat

 Chromosome 4A of wheat carries the Wx-B1 gene encoding the granule-bound starch synthase involved in amylose synthesis in the endosperm. To determine the pleiotropic effects of this locus and effects of independent QTLs on agronomic traits, genetical analysis of chromosome 4A was conducted using 98 single-chromosome recombinant substitution lines derived from a cross of Chinese Spring and Chinese Spring (Kanto107 4A) with a low amylose content due to the null Wx-B1b allele. For amylose content, most of the genetic variation was explained by the allelic difference at the Wx-B1 locus. An additional QTL of minor effect was mapped in the 6.2-cM Xbcd1738/Xcdo1387 interval on the short arm, where the allele from Kanto107 led to an increase in amylose content. Field trials over two seasons revealed a pleiotropic effect of Wx-B1, or else the effect of a closely linked QTL, on ear emergence time. A QTL linked to Wx-B1 was detected for plant height. For plant yield and its components, there was no evidence for significant main effects associated with Wx-B1 or adjacent regions. One plant-yield QTL was identified by RFLP markers on the short arm and this was identical to QTLs controlling spikelet number/ear and grain weight/ear. At these QTLs for agronomic traits, alleles from Kanto107 contributed to an earlier emergence time, a height reduction and an yield increase. Received: 10 August 1998 / Accepted: 3 November 1998     

Mapping quantitative trait loci for quality factors in an inter-class cross of US and Chinese wheat

Wheat quality factors are critical in determining the suitability of wheat (Triticum aestivum L.) for end-use product and economic value, and they are prime targets for marker-assisted selection. Objectives of this study were to identify quantitative trait loci (QTLs) that ultimately influence wheat market class and milling quality. A population of 132 F₁₂ recombinant inbred lines (RILs) was derived by single-seed descent from a cross between the Chinese hard wheat line Ning7840 and the soft wheat cultivar Clark and grown at three Oklahoma locations from 2001 to 2003. Milling factors such as test weight (volumetric grain weight, TW), kernel weight (KW), and kernel diameter (KD) and market class factors such as wheat grain protein content (GPC) and kernel hardness index (HI) were characterized on the basis of a genetic map constructed from 367 SSR and 241 AFLP markers covering all 21 chromosomes. Composite interval mapping identified eight QTLs for TW, seven for KW, six for KD, two each for GPC and HI measured by near-infrared reflectance (NIR) spectroscopy, and four for HI measured by single kernel characterization system. Positive phenotypic correlations were found among milling factors. Consistent co-localized QTLs were identified for TW, KW, and KD on the short arms of chromosomes 5A and 6A. A common QTL was identified for TW and KD on the long arm of chromosome 5A. A consistent major QTL for HI peaked at the Pinb-D1 locus on the short arm of chromosome 5D and explained up to 85% of the phenotypic variation for hardness. We identified QTLs for GPC on 4B and the short arm of 3A chromosomes. The consistency of quality factor QTLs across environments reveals their potential for marker-assisted selection.     

QTL analysis of agronomic traits in recombinant inbred lines of sunflower under partial irrigation

The objective of the present research was to map QTLs associated with agronomic traits such as days from sowing to flowering, plant height, yield and leaf-related traits in a population of recombinant inbred lines (RILs) of sunflower (Helianthus annuus). Two field experiments were conducted with well-irrigated and partially irrigated conditions in randomized complete block design with three replications. A map with 304 AFLP and 191 SSR markers with a mean density of 1 marker per 3.7 cM was used to identify QTLs related to the studied traits. The difference among RILs was significant for all studied traits in both conditions. Three to seven QTLs were found for each studied trait in both conditions. The percentage of phenotypic variance (R ²) explained by QTLs ranged from 4 to 49%. Three to six QTLs were found for each yield-related trait in both conditions. The most important QTL for grain yield per plant on linkage group 13 (GYP-P-13-1) under partial-irrigated condition controls 49% of phenotypic variance (R ²). The most important QTL for 1,000-grain weight (TGW-P-11-1) was identified on linkage group 11. Favorable alleles for this QTL come from RHA266. The major QTL for days from sowing to flowering (DSF-P-14-1) were observed on linkage group 14 and explained 38% of the phenotypic variance. The positive alleles for this QTL come from RHA266. The major QTL for HD (HD-P-13-1) was also identified on linkage group 13 and explained 37% of the phenotypic variance. Both parents (PAC2 and RHA266) contributed to QTLs controlling leaf-related traits in both conditions. Common QTL for leaf area at flowering (LAF-P-12-1, LAF-W-12-1) was detected in linkage group 12. The results emphasise the importance of the role of linkage groups 2, 10 and 13 for studied traits. Genomic regions on the linkage groups 9 and 12 are specific for QTLs of leaf-related traits in sunflower.     

Mapping of post-flowering drought resistance traits in grain sorghum: association between QTLs influencing premature senescence and maturity

The identification of genetic factors underlying the complex responses of plants to drought stress provides a solid basis for improving drought resistance. The stay-green character in sorghum (Sorghum bicolor L. Moench) is a post-flowering drought resistance trait, which makes plants resistant to premature senescence under drought stress during the grainfilling stage. The objective of this study was to identify quantitative trait loci (QTLs) that control premature senescence and maturity traits, and to investigate their association under post-flowering drought stress in grain sorghum. A genetic linkage map was developed using a set of recombinant inbred lines (RILs) obtained from the cross B35 × Tx430, which were scored for 142 restriction fragment length polymorphism (RFLP) markers. The RILs and their parental lines were evaluated for post-flowering drought resistance and maturity in four environments. Simple interval mapping identified seven stay-green QTLs and two maturity QTLs. Three major stay-green QTLs (SGA, SGD and SGG) contributed to 42% of the phenotypic variability (LOD 9.0) and four minor QTLs (SGB, SGI.1, SGI.2, and SGJ) significantly contributed to an additional 25% of the phenotypic variability in stay-green ratings. One maturity QTL (DFB) alone contributed to 40% of the phenotypic variability (LOD 10.0), while the second QTL (DFG) significantly contributed to an additional 17% of the phenotypic variability (LOD 4.9). Composite interval mapping confirmed the above results with an additional analysis of the QTL × Environment interaction. With heritability estimates of 0.72 for stay-green and 0.90 for maturity, the identified QTLs explained about 90% and 63% of genetic variability for stay-green and maturity traits, respectively. Although stay-green ratings were significantly correlated (r=0.22, P ≤ 0.05) with maturity, six of the seven stay-green QTLs were independent of the QTLs influencing maturity. Similarly, one maturity QTL (DFB) was independent of the stay-green QTLs. One stay-green QTL (SGG), however, mapped in the vicinity of a maturity QTL (DFG), and all markers in the vicinity of the independent maturity QTL (DFB) were significantly (P ≤ 0.1) correlated with stay-green ratings, confounding the phenotyping of stay-green. The molecular genetic analysis of the QTLs influencing stay-green and maturity, together with the association between these two inversely related traits, provides a basis for further study of the underlying physiological mechanisms and demonstrates the possibility of improving drought resistance in plants by pyramiding the favorable QTLs. Received: 10 October 1998 / Accepted: 12 July 1999     

Quantitative trait loci conferring grain mineral nutrient concentrations in durum wheat × wild emmer wheat RIL population

Mineral nutrient malnutrition, and particularly deficiency in zinc and iron, afflicts over 3 billion people worldwide. Wild emmer wheat, Triticum turgidum ssp. dicoccoides, genepool harbors a rich allelic repertoire for mineral nutrients in the grain. The genetic and physiological basis of grain protein, micronutrients (zinc, iron, copper and manganese) and macronutrients (calcium, magnesium, potassium, phosphorus and sulfur) concentration was studied in tetraploid wheat population of 152 recombinant inbred lines (RILs), derived from a cross between durum wheat (cv. Langdon) and wild emmer (accession G18-16). Wide genetic variation was found among the RILs for all grain minerals, with considerable transgressive effect. A total of 82 QTLs were mapped for 10 minerals with LOD score range of 3.2–16.7. Most QTLs were in favor of the wild allele (50 QTLs). Fourteen pairs of QTLs for the same trait were mapped to seemingly homoeologous positions, reflecting synteny between the A and B genomes. Significant positive correlation was found between grain protein concentration (GPC), Zn, Fe and Cu, which was supported by significant overlap between the respective QTLs, suggesting common physiological and/or genetic factors controlling the concentrations of these mineral nutrients. Few genomic regions (chromosomes 2A, 5A, 6B and 7A) were found to harbor clusters of QTLs for GPC and other nutrients. These identified QTLs may facilitate the use of wild alleles for improving grain nutritional quality of elite wheat cultivars, especially in terms of protein, Zn and Fe.     

Quantitative trait loci for yield and related traits in the wheat population Ning7840 × Clark

Grain yield and associated agronomic traits are important factors in wheat (Triticum aestivum L.) improvement. Knowledge regarding the number, genomic location, and effect of quantitative trait loci (QTL) would facilitate marker-assisted selection and the development of cultivars with desirable characteristics. Our objectives were to identify QTLs directly and indirectly affecting grain yield expression. A population of 132 F₁₂ recombinant inbred lines (RILs) was derived by single-seed descent from a cross between the Chinese facultative wheat Ning7840 and the US soft red winter wheat Clark. Phenotypic data were collected for 15 yield and other agronomic traits in the RILs and parental lines from three locations in Oklahoma from 2001 to 2003. Twenty-nine linkage groups, consisting of 363 AFLP and 47 SSR markers, were identified. Using composite interval mapping (CIM) analysis, 10, 16, 30, and 14 QTLs were detected for yield, yield components, plant adaptation (shattering and lodging resistance, heading date, and plant height), and spike morphology traits, respectively. The QTL effects ranged from 7 to 23%. Marker alleles from Clark were associated with a positive effect for the majority of QTLs for yield and yield components, but gene dispersion was the rule rather than the exception for this RIL population. Often, QTLs were detected in proximal positions for different traits. Consistent, co-localized QTLs were identified in linkage groups 1AL, 1B, 4B, 5A, 6A, and 7A, and less consistent but unique QTLs were identified on 2BL, 2BS, 2DL, and 6B. Results of this study provide a benchmark for future efforts on QTL identification for yield traits.     

QTL analysis of potato tuber dormancy

The potential loss of chemical sprout inhibitors because of public concern over the use of pesticides underscores the desirability of breeding for long dormancy of potato (Solanum tuberosum L.) tubers. Quantitative trait locus (QTL) analyses were performed in reciprocal backcrosses between S. tuberosum and S. berthaultii toward defining the complexity of dormancy. S. berthaultii is a wild Bolivian species characterized by a short-day requirement for tuberization, long tuber dormancy, and resistance to several insect pests. RFLP alleles segregating from the recurrent parents as well as from the interspecific hybrid were monitored in two segregating progenies. We detected QTLs on nine chromosomes that affected tuber dormancy, either alone or through epistatic interactions. Alleles from the wild parent promoted dormancy, with the largest effect at a QTL on chromosome 2. Long dormancy appeared to be recessive in the backcross to S. berthaultii (BCB). In BCB the additive effects of dormancy QTLs accounted for 48% of the measured phenotypic variance, and adding epistatic effects to the model explained only 4% more. In contrast, additive effects explained only 16% of the variance in the backcross to S. tuberosum (BCT), and an additional 24% was explained by the inclusion of epistatic effects. In BCB variation at all QTLs detected was associated with RFLP alleles segregating from the hybrid parent; in BCT all QTLs except for two found through epistasis were detected through RFLP alleles segregating from the recurrent parent. At least three dormancy QTLs mapped to markers previously found to be associated with tuberization in these crosses.Paper number 55 of the Department of Fruit and Vegetable Science, Cornell University     

Dynamic quantitative trait locus analysis of seed dormancy at three development stages in rice

In this study, a rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of seed dormancy (SD) at 4 (early), 5 (middle) and 6 (late) weeks after heading stages. Dynamic analysis showed that the indica IR28 variety tended to have deeper dormancy than the japonica Daguandao at the middle and late development stages. The level of SD decreased with the process of seed development. The significant interaction between heading date (HD) and SD occurred only in those seeds collected at the early development stage. A total of nine additive quantitative trait loci (QTLs) and eight epistatic QTLs for SD were identified at three seed development stages. Of them, one additive and four epistatic QTLs were identified for the early stage, six additive and one epistatic QTL for the middle stage and two additive and three epistatic QTLs for the late stage. The phenotypic variation explained by each additive and epistatic QTL ranged from 5.8 to 30.6 % and from 3.8 to 13.1 %, respectively. Compared with the additive QTLs, epistatic interactions were much more important for SD at the early and late development stages. Two major additive QTLs, qSD3.1 and qSD4.1, were identified; each QTL could explain more than 20 % of the total phenotypic variance and each dormancy-enhancing allele could decrease the germination percentage by about 10 %. By comparing the chromosomal positions of these additive QTLs with those previously identified, five additive QTLs, qSD1.2, qSD2.1, qSD3.2, qSD4.1 and qSD9.1, might represent novel genes. One QTL identified here, qHD1, and nine QTLs identified in previous studies for HD were co-located with our QTLs for SD, which indicated that the significant correlation between SD and HD might be due to the linkage of QTLs for SD and HD. Four RILs with deep dormancy at development stages but non-dormancy after post-ripening under different germination conditions were selected. Using the selected RILs, three cross combinations of SD for the development of RIL populations were predicted. The selected RILs and the identified QTLs might be applicable for the improvement of pre-harvest sprouting tolerance by marker-assisted selection in rice.     

Mapping QTLs for alpha-amylase activity in rye grain

Genetic control of alpha-amylase activity in rye grain was investigated by QTL mapping based on DS2 x RXL10 intercross consisting of 99 F5-6 families propagated at one location during four vegetation seasons. A wide range of variation in alpha-amylase activity and transgression effects were found among families and parental lines. This variation was shown to be determined in 40.1% by 7 significant (LOD score not less than 2.5) and 2 putative QTLs (2 < LOD < 2.5) distributed on all rye chromosomes except 4R. Two significant QTLs located on 3RL and 5RL chromosome arms were expressed each year. The third significant QTL was detected in three years (1RL). The other four significant QTLs (2RL, 5RS, 6RL, 7RL) were found in one year of study. The number and composition of QTLs were specific for a given year varying from three to six. QTLs were not correlated with isoenzyme polymorphisms at the structural alpha-Amy1 loci. A QTL associated with a region containing the alpha-Amy3 locus was detected on chromosome 5RL. Both high- and low-activity QTL alleles were found in each parental line, which explains the appearance of transgressive recombinants in the segregating population.     

Mapping of quantitative trait loci for basmati quality traits in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

Traditional basmati rice varieties are very low yielding due to their poor harvest index, tendency to lodging and increasing susceptibility to foliar diseases; hence there is a need to develop new varieties combining the grain quality attributes of basmati with high yield potential to fill the demand gap. Genetic control of basmati grain and cooking quality traits is quite complex, but breeding work can be greatly facilitated by use of molecular markers tightly linked to these traits. A set of 209 recombinant inbred lines (RILs) developed from a cross between basmati quality variety Pusa 1121 and a contrasting quality breeding line Pusa 1342, were used to map the quantitative trait loci (QTLs) for seven important quality traits namely grain length (GL), grain breadth (GB), grain length to breadth ratio (LBR), cooked kernel elongation ratio (ELR), amylose content (AC), alkali spreading value (ASV) and aroma. A framework molecular linkage map was constructed using 110 polymorphic simple sequence repeat (SSR) markers distributed over the 12 rice chromosomes. A number of QTLs, including three for GL, two for GB, two for LBR, three for aroma and one each for ELR, AC and ASV were mapped on seven different chromosomes. While location of majority of these QTLs was consistent with the previous reports, one QTL for GL on chromosomes 1, and one QTL each for ELR and aroma on chromosomes 11 and 3, respectively, are being reported here for the first time. Contrary to the earlier reports of monogenic recessive inheritance, the aroma in Pusa 1121 is controlled by at least three genes located on chromosomes 3, 4 and 8, and similar to the reported association of badh2 gene with aroma QTL on chromosome 8, we identified location of badh1 gene in the aroma QTL interval on chromosome 4. A discontinuous 5 + 3 bp deletion in the seventh exon of badh2 gene, though present in all the RILs with high aroma, was not sufficient to impart this trait to the rice grains as many of the RILs possessing this deletion showed only mild or no aroma expression. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A wheat homolog of MOTHER OF FT AND TFL1 acts in the regulation of germination

Seed dormancy is an adaptive mechanism and an important agronomic trait. Temperature during seed development strongly affects seed dormancy in wheat (Triticum aestivum) with lower temperatures producing higher levels of seed dormancy. To identify genes important for seed dormancy, we used a wheat microarray to analyze gene expression in embryos from mature seeds grown at lower and higher temperatures. We found that a wheat homolog of MOTHER OF FT AND TFL1 (MFT) was upregulated after physiological maturity in dormant seeds grown at the lower temperature. In situ hybridization analysis indicated that MFT was exclusively expressed in the scutellum and coleorhiza. Mapping analysis showed that MFT on chromosome 3A (MFT-3A) colocalized with the seed dormancy quantitative trait locus (QTL) QPhs.ocs-3A.1. MFT-3A expression levels in a dormant cultivar used for the detection of the QTL were higher after physiological maturity; this increased expression correlated with a single nucleotide polymorphism in the promoter region. In a complementation analysis, high levels of MFT expression were correlated with a low germination index in T1 seeds. Furthermore, precocious germination of isolated immature embryos was suppressed by transient introduction of MFT driven by the maize (Zea mays) ubiquitin promoter. Taken together, these results suggest that MFT plays an important role in the regulation of germination in wheat.