Inheritance and biochemical basis of yellowing of apical leaves: a unique trait in chickpea (Cicer arietinum L.)

A unique trait, i.e. yellowing of apical/young leaves in response to low temperature and high relative humidity was identified in a chickpea genotype, ICCX110069. To determine inheritance pattern of this trait, ICCX110069 was crossed to four other genotypes, GL14050, GL14049, GL14059 and SAGL152117, that exhibited normal green apical leaves under similar environmental conditions. The F₁, F₂, F₃, BC₁F₁ and BC₁F₂ generations were generated. A ratio of 13 normal green leaf: three yellow leaf was found to be the best fit, indicated digenic gene action with suppressor effect of normal green leaf over the expression of yellowing of apical/young leaf trait. The chlorophyll content was significantly lower, while guaiacol peroxidase activity was significantly higher in yellow leaves of ICCX110069 as compared to green leaves of the same genotype and of GL14049, indicating the competence of antioxidative defence mechanism involved with the expression of this trait.

Co-existence of Leclercia adecarboxylata (LSE-1) and Bradyrhizobium sp. (LSBR-3) in nodule niche for multifaceted effects and profitability in soybean production

The present study was designed with the objective of improving growth and nodulation of soybean [Glycine max (L.) Merill] with co-inoculation of native Bradyrhizobium sp. (LSBR-3) (KF906140) and non-rhizobial nodule endophytic diazotroph Leclercia adecarboxylata (LSE-1) (KX925974) with multifunctional plant growth promoting (PGP) traits in cereal based cropping system (Rice-Wheat). A total of 40 endophytic bacteria from cultivated and wild sp. of soybean were screened for multifarious PGP traits and pathogenicity test. Based on PGP traits, antagonistic activities and bio-safety test; L. adecarboxylata (LSE-1) was identified with 16 S rRNA gene sequencing along with the presence of nifH (nitrogen fixation) and ipdc (IAA production) genes. Dual inoculant LSE-1 and LSBR-3 increased indole acetic acid (IAA), P & Zn-solubilization, 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity, siderophore, biofilm formation and exo-polysaccharides in contrast to single inoculation treatment. Further, assessment of dual inoculant LSBR-3 + LSE-1 improved growth parameters, nodulation, soil enzymes activities, nutrient accumulation and yield as compared to single as well as un-inoculated control treatment under field conditions. Single inoculant LSBR-3 improved yield by 8.84% over control. Further, enhancement of 4.15% grain yield was noticed with LSBR-3 + LSE-1 over LSBR-3 alone treatment. Application of LSBR-3 + LSE-1 gave superior B:C ratio (1.29) and additional income approximately 116 USD ha-1 in contrast to control treatment. The present results thus, is the first report of novel endophytic diazotroph L. adecarboxylata (LSE-1) as PGPR from Indian conditions particularly in Punjab region for exploiting as potential PGPR along with Bradyrhizobium sp. (LSBR-3) in soybean.

A population-based cross-sectional study to determine the practices of breastfeeding among the lactating mothers of Patiala city

Introduction:

The present study was undertaken to study the breastfeeding practices and the influence of literacy and prevailing cultural factors on different aspects of breastfeeding.

Materials and Methods:

A community-based cross-sectional study was conducted at Badungar, a semi-urban area in Patiala city including a total of 370 mothers. Mothers were interviewed using pre-formed, semi-structured Performa. The participant's demographic information, awareness and practices regarding breastfeeding were recorded by paying house to house visits. Data were analyzed using SPSS ver. 21.

Results:

Only 27.30% of the mothers knew that breastfeeding should be initiated within 1 hour of birth. A total of 51.62% mothers considered prelacteal feed to be the right practice while 55.95% considered colostrum bad for the baby. Only 53.78% of the lactating mothers knew the correct meaning of exclusive breastfeeding. Only 24.86% mothers started breastfeeding within an hour after birth. Colostrum was not given by 57.29% of the lactating mothers while Prelacteal feeds were given by 50.81% mothers. Exclusive breastfeeding till 6 months was given by 45.67% mothers. A significant association was observed in high mother's education, high socio-economic status, nuclear status of family, history of antenatal care registration, and hospital delivery with exclusive breastfeeding (P < 0.01).

Conclusion:

Study concluded that breastfeeding practices were not optimum; hence promotion of knowledge regarding the right practices of breastfeeding and focus on the factors affecting them is highly warranted in this area.

Alien chromosome segment from Aegilops speltoides and Dasypyrum villosum increases drought tolerance in wheat via profuse and deep root system

BACKGROUND

Recurrent drought associated with climate change is a major constraint to wheat (Triticum aestivum L.) productivity. This study aimed to (i) quantify the effects of addition/substitution/translocation of chromosome segments from wild relatives of wheat on the root, physiological and yield traits of hexaploid wheat under drought, and (ii) understand the mechanism(s) associated with drought tolerance or susceptibility in wheat-alien chromosome lines.

METHODS

A set of 48 wheat-alien chromosome lines (addition/substitution/translocation lines) with Chinese Spring background were used. Seedling root traits were studied on solid agar medium. To understand the influence of drought on the root system of adult plants, these 48 lines were grown in 150-cm columns for 65 d under full irrigation or withholding water for 58 d. To quantify the effect of drought on physiological and yield traits, the 48 lines were grown in pots under full irrigation until anthesis; after that, half of the plants were drought stressed by withholding water for 16 d before recording physiological and yield-associated traits.

RESULTS

The alien chromosome lines exhibited altered root architecture and decreased photochemical efficiency and seed yield and its components under drought. The wheat-alien chromosome lines T5DS·5S#3L (TA5088) with a chromosome segment from Aegilops speltoides (5S) and T5DL.5 V#3S (TA5638) with a chromosome segment from Dasypyrum villosum (5 V) were identified as drought tolerant, and the drought tolerance mechanism was associated with a deep, thin and profuse root system.

CONCLUSIONS

The two germplasm lines (TA5088 and TA5638) could be used in wheat breeding programs to improve drought tolerance in wheat and understand the underlying molecular genetic mechanisms of root architecture and drought tolerance.

Synergism of Pseudomonas aeruginosa (LSE-2) nodule endophyte with Bradyrhizobium sp. (LSBR-3) for improving plant growth, nutrient acquisition and soil health in soybean

The present study was aimed to assess the scope of native potential endophyte Pseudomonas aeruginosa (LSE-2) strain (KX925973) with recommended Bradyrhizobium sp. (LSBR-3) (KF906140) for synergistic effect to develop as consortium biofertilizer of soybean. A total of 28 non-rhizobial endophytic bacteria were isolated from cultivated and wild sp. of soybean. All isolates were screened for multifarious PGP traits viz. Indole-3-acetic acid (IAA), phosphate (P) and zinc (Zn) solubilization, siderophore, cell wall degrading enzymes and pathogenicity. Compatible of LSBR-3 and LSE-2 enhanced IAA, P-solubilization, 1-aminocyclopropane-carboxylate deaminase and biofilm formation over the single inoculant treatment. Further, consortium was evaluated in vivo for growth, symbiotic traits, nutrient acquisition, soil quality parameters and yield attributes of soybean. Improvement in growth parameters were recorded with dual inoculant LSBR-3 + LSE-2 as compared to LSBR-3 alone and un-inoculated control treatments. Significantly (p ≥ 0.05) high symbiotic and soil quality parameters (phosphatase and soil dehydrogenase activity) was recorded with LSBR-3 + LSE-2 at vegetative and flowering stage as compared to LSBR-3 alone and un-inoculated control treatments. Single inoculation of LSBR-3 improved grain yield by 4.25% over the un-inoculated control treatment, further, enhancement in yield was recorded with consortium inoculant (LSBR-3 and LSE-2) by 3.47% over the LSBR-3 alone. Application of consortium inoculant (LSBR-3 + LSE-2) gave an additional income of Rs. 5089/ha over the un-inoculated control treatment. The results, thus strongly suggest that endophytic diazotroph LSE-2 can be used as potent bio-inoculant along with LSBR-3 as bio-enhancer for improving soybean productivity in a sustainable system.

Multiplate and TEG platelet mapping in a population of severely injured trauma patients

OBJECTIVES

The objectives of this study were to compare thromboelastography platelet mapping (TEG PM) with impedance aggregometry (Multiplate, MP) in a single trauma population and relate their results clinically.

BACKGROUND

Platelet function as measured by thromboelastography and impedance aggregometry demonstrates significant reductions that persist for days following traumatic injury. However, no study compares these devices and the correlation between them is not known.

METHODS

In level 1 trauma patients, TEG PM and MP were conducted at their initial presentation to the emergency department. Within-device repeatability and between-device association were determined using correlation analyses. Demographic variables, Injury Severity Score, blood product transfusion, laboratory test results and mortality rate were recorded.

RESULTS

Ninety-two patients were enrolled. Within-device repeatability was high for TEG PM and MP for arachidonic acid (AA) and adenosine diphosphate (ADP) activation pathways. When comparing TEG PM with MP, results correlated poorly in the ADP pathway (Spearman's rho = 0·11, P = 0·44) and moderately in the AA pathway (Spearman's rho = 0·56, P < 0·0001). TEG PM was predictive of blood product transfusion and correlated with increased base deficit, whereas MP was only predictive of mortality.

CONCLUSIONS

Intra-device variability was low for TEG PM and MP, but the two point-of-care devices measuring platelet function correlate poorly with each other in injured trauma patients. Each device also had different clinical associations.

Linkage mapping of Mungbean yellow mosaic India virus (MYMIV) resistance gene in soybean

Mungbean Yellow Mosaic India Virus (MYMIV) is one of the most prevalent pathogen that limits soybean production in India. In this study RILs derived from JS335, dominant but MYMIV susceptible variety and PI171443, donor of MYMIV resistance gene in most of the MYMIV resistant varieties released in India and F2 population derived from SL525, a resistant variety released for northern India and NRC101, a susceptible genotype were used to study the inheritance of MYMIV resistance and map the gene responsible for MYMIV resistance. F1s were found to be completely susceptible. F_2:3 and RILs population segregated to fit a ratio of 1:2:1 and 1:1 indicating that a single recessive gene controlled resistance to MYMIV. BSA was performed using 144 polymorphic SSR markers. MYMIV resistance gene was mapped on chr 6 (LG C2) within a 3.5-cM genome region between two SSR markers GMAC7L and Satt322 whose size was estimated to be 77.115 kb (position of 12,259,594-12,336,709 bp). This is the first report on linkage mapping of MYMIV resistance gene in soybean. This will be helpful in breeding soybean varieties for resistance against MYMIV responsible for wide spread damage to soybean crop in India using Marker Assisted Selection.

Crop-ecology and nutritional variability influence growth and secondary metabolites of Stevia rebaudiana Bertoni

BACKGROUND

Plant nutrition and climatic conditions play important roles on the growth and secondary metabolites of stevia (Stevia rebaudiana Bertoni); however, the nutritional dose is strongly governed by the soil properties and climatic conditions of the growing region. In northern India, the interactive effects of crop ecology and plant nutrition on yield and secondary metabolites of stevia are not yet properly understood. Thus, a field experiment comprising three levels of nitrogen, two levels of phosphorus and three levels of potassium was conducted at three locations to ascertain whether the spatial and nutritional variability would dominate the leaf yield and secondary metabolites profile of stevia.

RESULTS

Principal component analysis (PCA) indicates that the applications of 90 kg N, 40 kg P2O5 and 40 kg K2O ha-1 are the best nutritional conditions in terms of dry leaf yield for CSIR-IHBT (Council of Scientific and Industrial Research- Institute Himalayan Bioresource Technology) and RHRS (Regional Horticultural Research Station) conditions. The spatial variability also exerted considerable effect on the leaf yield and stevioside content in leaves. Among the three locations, CSIR-IHBT was found most suitable in case of dry leaf yield and secondary metabolites accumulation in leaves.

CONCLUSIONS

The results suggest that dry leaf yield and accumulation of stevioside are controlled by the environmental factors and agronomic management; however, the accumulation of rebaudioside-A (Reb-A) is not much influenced by these two factors. Thus, leaf yield and secondary metabolite profiles of stevia can be improved through the selection of appropriate growing locations and proper nutrient management.

MRI and PET-CT: Comparison in post-treatment evaluation of head and neck squamous cell carcinomas

BACKGROUND

Treatment of patients with head and neck cancers includes surgery, radiation therapy and chemotherapy due to which the complex anatomy in this region is further complicated by post surgical or radiation changes making the distinction between post therapy changes and recurrence or residual tumor challenging. We decided to compare the diagnostic performance of FDG-PET/CT and MRI scans in the response assessment of patients with Head and Neck Squamous Cell Carcinomas (HNSCC).

METHODS

Fifty consecutive patients with carcinoma of the head and neck region undergoing treatment at our center were enrolled in the study and evaluated with both MRI scan and PET-CT scan at presentation, at 12 weeks after treatment and at 24 weeks post-treatment.

RESULTS

Post treatment evaluation at 24 weeks revealed a sensitivity, specificity, PPV, NPV of 95.83%, 82.37%, 78.91%, 96.3% for MRI respectively while corresponding values for PET-CT scans were 95.83%, 91.97%, 85.45% and 96.3%. Evaluation by treatment modality showed a concurrence rate of positive biopsies of 71.33% and 74.54% respectively for MRI and PET-CT scans in surgical patients, 93.33% and 91.25% respectively for the chemo-radiotherapy and 71.43% and 85.71% respectively for patients treated with surgery and radiotherapy.

CONCLUSION

In our study, both modalities were useful for evaluation at 12 weeks, however by 24 weeks PET-CT was superior. Both the modalities suffer from high negative predictive values and relatively low positive predictive values. These persisted irrespective of the treatment modality with MRI being slightly better for patients on chemo-radiotherapy while PET-CT scans were better if surgery was one of the modalities of treatment.

Sequence organization and evolutionary dynamics of Brachypodium-specific centromere retrotransposons

Brachypodium distachyon is a wild annual grass belonging to the Pooideae, more closely related to wheat, barley, and forage grasses than rice and maize. As an experimental model, the completed genome sequence of B. distachyon provides a unique opportunity to study centromere evolution during the speciation of grasses. Centromeric satellite sequences have been identified in B. distachyon, but little is known about centromeric retrotransposons in this species. In the present study, bacterial artificial chromosome (BAC)-fluorescence in situ hybridization was conducted in maize, rice, barley, wheat, and rye using B. distachyon (Bd) centromere-specific BAC clones. Eight Bd centromeric BAC clones gave no detectable fluorescence in situ hybridization (FISH) signals on the chromosomes of rice and maize, and three of them also did not yield any FISH signals in barley, wheat, and rye. In addition, four of five Triticeae centromeric BAC clones did not hybridize to the B. distachyon centromeres, implying certain unique features of Brachypodium centromeres. Analysis of Brachypodium centromeric BAC sequences identified a long terminal repeat (LTR)-centromere retrotransposon of B. distachyon (CRBd1). This element was found in high copy number accounting for 1.6 % of the B. distachyon genome, and is enriched in Brachypodium centromeric regions. CRBd1 accumulated in active centromeres, but was lost from inactive ones. The LTR of CRBd1 appears to be specific to B. distachyon centromeres. These results reveal different evolutionary events of this retrotransposon family across grass species.

Genome differentiation in Aegilops. 2. Physical mapping of 5S and 18S-26S ribosomal RNA gene families in diploid species

The distribution of the 5S and 18S-5.8S-26S (18S-26S) ribosomal RNA (rRNA) gene families on chromosomes of all diploid Aegilops species was studied by in situ hybridization with pTa71 (18S-26S rDNA) and pTa794 (5S rDNA) DNA clones. One major 18S-26S rDNA locus was found in the nucleolus organizer region (NOR) of each of the species Aegilops tauschii and Aegilops uniaristata and two loci were detected in the remaining species. In addition to major NORs, from one to nine minor loci were observed; their numbers and chromosomal locations were species-specific. Some minor loci were polymorphic, whereas others were conserved. One or two 5S rDNA loci were observed in the short arms of the chromosomes of groups 1 and 5 of all diploid Aegilops species except Ae. uniaristata, where one 5S rDNA site was located in the distal part of the long arm of chromosome 1N. The 5S rDNA loci were not associated with NORs; however, the relative positions of two ribosomal RNA gene families were diagnostic for chromosomes of homoeologous groups 1, 5, and 6. Implications of these results for establishing phylogenetic relationships of diploid Aegilops species and mechanisms of genome differentiation are discussed. Key words : wheat, Triticum, Aegilops, 5S rRNA, 18S-26S rRNA, in situ hybridization, evolution.

Nonisotopic in situ hybridization and plant genome mapping: the first 10 years

Nonisotopic in situ hybridization (ISH) was introduced in plants in 1985. Since then the technique has been widely used in various areas of plant genome mapping. ISH has become a routine method for physical mapping of repetitive DNA sequences and multicopy gene families. ISH patterns on somatic metaphase chromosomes using tandemly repeated sequences provide excellent physical markers for chromosome identification. Detection of low or single copy sequences were also reported. Genomic in situ hybridization (GISH) was successfully used to analyze the chromosome structure and evolution of allopolyploid species. GISH also provides a powerful technique for monitoring chromatin introgession during interspecific hybridization. A sequential chromosome banding and ISH technique was developed. The sequential technique is very useful for more precise and efficient mapping as well as cytogenetic determination of genomic affinities of individual chromosomes in allopolyploid species. A critical review is made on the present resolution of the ISH technique and the future outlook of ISH research is discussed.

Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat

Group 1 chromosomes of the Triticeae tribe have been studied extensively because many important genes have been assigned to them. In this paper, chromosome 1 linkage maps of Triticum aestivum, T. tauschii, and T. monococcum are compared with existing barley and rye maps to develop a consensus map for Triticeae species and thus facilitate the mapping of agronomic genes in this tribe. The consensus map that was developed consists of 14 agronomically important genes, 17 DNA markers that were derived from known-function clones, and 76 DNA markers derived from anonymous clones. There are 12 inconsistencies in the order of markers among seven wheat, four barley, and two rye maps. A comparison of the Triticeae group 1 chromosome consensus map with linkage maps of homoeologous chromosomes in rice indicates that the linkage maps for the long arm and the proximal portion of the short arm of group 1 chromosomes are conserved among these species. Similarly, gene order is conserved between Triticeae chromosome 1 and its homoeologous chromosome in oat. The location of the centromere in rice and oat chromosomes is estimated from its position in homoeologous group 1 chromosomes of Triticeae.

Molecular cytogenetic analysis of Agropyron chromatin specifying resistance to barley yellow dwarf virus in wheat

Nine families of bread wheat (TC5, TC6, TC7, TC8, TC9, TC10, TC14, 5395-(243AA), and 5395) with resistance to barley yellow dwarf virus and containing putative translocations between wheat and a group 7 chromosome of Agropyron intermedium (L1 disomic addition line, 7Ai#1 chromosome) induced by homoeologous pairing or tissue culture were analyzed. C-banding, genomic in situ hybridization (GISH), and restriction fragment length polymorphism (RFLP) in combination with repetitive Agropyron-specific sequences and deletion mapping in wheat were used to determine the relative locations of the translocation breakpoints and the size of the transferred alien chromatin segments in hexaploid wheat-Agropyron translocation lines. All homoeologous compensating lines had complete 7Ai#1 or translocated 7Ai#1-7D chromosomes that substitute for chromosome 7D. Two complete 7Ai#1 (7D) substitution lines (5395-(243AA) and 5395), one T1BS-7Ai#1S&#x2219;7Ai#1L addition line (TC7), and two different translocation types, T7DS-7Ai#1S&#x2219;7Ai#1L (TC5, TC6, TC8, TC9, and TC10) and T7DS&#x2219;7DL-7Ai#1L (TC14), substituting for chromosome 7D were identified. The substitution line 5395-(243AA) had a reciprocal T1BS&#x2219;1BL-4BS/T1BL-4BS&#x2219;4BL translocation. TC14 has a 6G (6B) substitution. The RFLP data from deletion mapping studies in wheat using 37 group 7 clones provided 10 molecular tagged chromosome regions for homoeologous and syntenic group 7 wheat or Agropyron chromosomes. Together with GISH we identified three different sizes of the transferred Agropyron chromosome segments with approximate breakpoints at fraction length (FL) 0.33 in the short arm of chromosome T7DS-7Ai#1S&#x2219;7Ai#1L (TC5, TC6, TC8, TC9, and TC10) and another at FL 0.37 of the nonhomoeologous translocated chromosome T1BS-7Ai#1S&#x2219;7Ai#1L (TC7). One breakpoint was identified in the long arm of chromosome T7DS&#x2219;7DL-7Ai#1L (TC14) at FL 0.56. We detected some nonreciprocal translocations for the most proximal region of the chromosome arm of 7DL, which resulted in small duplications. Key words : C-banding, genomic in situ hybridization (GISH), physical mapping, translocation mapping, RFLP analysis.

Alloplasmic wheat - Elymus ciliaris chromosome addition lines

Alloplasmic euploid wheat with the cytoplasm of Elymus ciliaris (2n = 4x = 28, ScScYcYc) is male sterile and has reduced vigor. However, alloplasmic plants with E. ciliaris chromosomes 1Sc or 1Yc marked by gliadin genes Gli-Sc1 and Gli-Ycl, respectively, are vigorous and fertile. The Rf genes on 1Sc and 1Yc are named Rf-Sc1 and Rf-Yc1. Two chromosome translocations involving 1Yc were isolated. The first involved the short arm of 1Yc translocated to the short arm of wheat chromosome 3B. The second involved the short arm of 1Yc translocated to the short arm of a chromosome, designated L, of E. ciliaris. The second line also has another E. ciliaris chromosome designated A and lacks wheat chromosome 6A. This line is resistant to Puccinia recondita. The relationship between fertility restoration and nucleolar organizing regions is discussed. Key words : Triticum aestivum, Elymus ciliaris, chromosome addition, Rf genes, nucleolar organizing regions.

Genome differentiation in Aegilops. 1. Distribution of highly repetitive DNA sequences on chromosomes of diploid species

Genome differentiation in 12 diploid Aegilops species was analyzed using in situ hybridization with the highly repetitive DNA sequences pSc119 and pAs1 and C-banding. Chromosomes of all these diploid Aegilops species hybridized with the pSc119 probe; however, the level of hybridization and labeling patterns differed among genomes. Only four species (Ae. squarrosa, Ae. comosa, Ae. heldreichii, and Ae. uniaristata) showed distinct hybridization with pAs1. The labeling patterns were species-specific and chromosome-specific. Differences in in situ hybridization (ISH) patterns, also observed by C-banding, exist between the karyotypes of Ae. comosa and Ae. heldreichii, suggesting that they are separate, although closely related, subspecies. The S genome of Ae. spelioides was most similar to the B and G genomes of polyploid wheats on the basis of both C-banding and ISH patterns, but was different from other species of section Sitopsis. These species had different C-banding patterns but they were similar to each other and to Ae. mutica in the distribution of pSc119 hybridization sites. Two types of labeling were detected in Ae. squarrosa with the pAs1 probe. The first resembled that of the D-genome chromosomes of bread wheat, Triticum aestivum L. em. Thell., while the second was similar to the D genome of some of the polyploid Aegilops species. Relationships among diploid Aegilops species and the possible mechanisms of genome differentiation are discussed. Key words : wheat, Triticum, Aegilops, in situ hybridization, C-banding, evolution.

Sequential chromosome banding and in situ hybridization analysis

Different combinations of chromosome N- or C-banding with in situ hybridization (ISH) or genomic in situ hybridization (GISH) were sequentially performed on metaphase chromosomes of wheat. A modified N-banding-ISH/GISH sequential procedure gave best results. Similarly, a modified C-banding - ISH/GISH procedure also gave satisfactory results. The variation of the hot acid treatment in the standard chromosome N- or C-banding procedures was the major factor affecting the resolution of the subsequent ISH and GISH. By the sequential chromosome banding - ISH/GISH analysis, multicopy DNA sequences and the breakpoints of wheat-alien translocations were directly allocated to specific chromosomes of wheat. The sequential chromosome banding- ISH/GISH technique should be widely applicable in genome mapping, especially in cytogenetic and molecular mapping of heterochromatic and euchromatic regions of plant and animal chromosomes.

Characterization of Hordeum chilense chromosomes by C-banding and in situ hybridization using highly repeated DNA probes

C-banding patterns of Hordeum chilense and of Triticum aestivum 'Chinese Spring' - H. chilense disomic addition lines were analyzed and compared with in situ hybridization patterns using a biotin-labeled highly repetitive Triticum tauschii DNA sequence, pAs1, and a wheat 18S-26S rDNA probe. All seven H. chilense chromosomes pairs and the added H. chilense chromosomes present in the addition lines were identified by their characteristic C-banding pattern. Chromosome morphology and banding patterns were similar to those of the corresponding chromosomes present in the parent H. chilense accession. A C-banded karyotype of the added H. chilense chromosomes was constructed and chromosome lengths, arm ratios, and relative length, as compared with chromosome 3B, were determined. The probe pAs1 was found to hybridize to specific areas on telomeres and interstitial sites along the chromosomes, allowing the identification of all seven pairs of the H. chilense chromosomes. Comparison of the patterns of distribution of the hybridization sites of clone pAs1 in the T. tauschii and H. chilense chromosomes was carried out by in situ hybridization on somatic metaphase chromosomes of the HchHchDD amphiploid. In situ hybridization using the 18S-26S rDNA probe confirmed that the H. chilense chromosomes 5Hch and 6Hch were carrying nucleolus organizer regions. The results are discussed on the basis of phylogenetic relationships between D and Hch genomes.

A cytogenetically based physical map of chromosome 1B in common wheat

We have constructed a cytogenetically based physical map of chromosome 1B in common wheat by utilizing a total of 18 homozygous deletion stocks. It was possible to divide chromosome 1B into 17 subregions. Nineteen genetic markers are physically mapped to nine subregions of chromosome 1B. Comparison of the cytological map of chromosome 1B with an RFLP-based genetic linkage map of Triticum tauschii revealed that the linear order of the genetic markers was maintained between chromosome 1B of hexaploid wheat and 1D of T. tauschii. Striking differences were observed between the physical and genetic maps in relation to the relative distances between the genetic markers. The genetic markers clustered in the middle of the genetic map were physically located in the distal regions of both arms of chromosome 1B. It is unclear whether the increased recombination in the distal regions of chromosome 1B is due to specific regions of increased recombination or a more broadly distributed increase in recombination in the distal regions of Triticeae chromosomes.

Genomic in situ hybridization differentiates between A/D- and C-genome chromatin and detects intergenomic translocations in polyploid oat species (genus Avena)

The genomic in situ hybridization (GISH) technique was used to discriminate between chromosomes of the C genome and those of the A and A/D genomes in allopolyploid oat species (genus Avena). Total biotinylated DNA from A. strigosa (2n = 2x = 14, AsAs genome) was mixed with sheared, unlabelled total DNA from A. eriantha (2n = 2x = 14, CpCp) at a ratio of 1:200 (labelled to unlabelled). The resulting hybridization pattern consisted of 28 mostly labelled and 14 mostly unlabelled chromosomes in the hexaploids. Attempts to discriminate between chromosomes of the A and D genomes in A. sativa (2n = 6x = 42, AACCDD) were unsuccessful using GISH. At least eight intergenomic translocation segments were detected in A. sativa 'Ogle', several of which were not observed in A. byzantina 'Kanota' (2n = 6x = 42, AACCDD) or in A. sterilis CW 439-2 (2n = 6x = 42, AACCDD). At least five intergenomic translocation segments were observed in A. maroccana CI 8330 'Magna' (2n = 4x = 28, AACC). In both 'Ogle' and 'Magna', positions of most of these translocations matched with C-banding patterns.

A novel Robertsonian translocation event leads to transfer of a stem rust resistance gene (Sr52) effective against race Ug99 from Dasypyrum villosum into bread wheat

Stem rust (Puccinia graminis f. sp. tritici Eriks. & E. Henn.) (the causal agent of wheat stem rust) race Ug99 (also designated TTKSK) and its derivatives have defeated several important stem rust resistance genes widely used in wheat (Triticum aestivum L.) production, rendering much of the worldwide wheat acreage susceptible. In order to identify new resistance sources, a large collection of wheat relatives and genetic stocks maintained at the Wheat Genetic and Genomic Resources Center was screened. The results revealed that most accessions of the diploid relative Dasypyrum villosum (L.) Candargy were highly resistant. The screening of a set of wheat-D. villosum chromosome addition lines revealed that the wheat-D. villosum disomic addition line DA6V#3 was moderately resistant to race Ug99. The objective of the present study was to produce and characterize compensating wheat-D. villosum whole arm Robertsonian translocations (RobTs) involving chromosomes 6D of wheat and 6V#3 of D. villosum through the mechanism of centric breakage-fusion. Seven 6V#3-specific EST-STS markers were developed for screening F(2) progeny derived from plants double-monosomic for chromosomes 6D and 6V#3. Surprisingly, although 6D was the target chromosome, all recovered RobTs involved chromosome 6A implying a novel mechanism for the origin of RobTs. Homozygous translocations (T6AS·6V#3L and T6AL·6V#3S) with good plant vigor and full fertility were selected from F(3) families. A stem rust resistance gene was mapped to the long arm 6V#3L in T6AS·6V#3L and was designated as Sr52. Sr52 is temperature-sensitive and is most effective at 16°C, partially effective at 24°C, and ineffective at 28°C. The T6AS·6V#3L stock is a new source of resistance to Ug99, is cytogenetically stable, and may be useful in wheat improvement.

Genetic compensation abilities of Aegilops speltoides chromosomes for homoeologous B-genome chromosomes of polyploid wheat in disomic S(B) chromosome substitution lines

The S genome of Aegilops speltoides is closely related to the B and G genomes of polyploid wheats. However, little work has been reported on the genetic relationships between the S-genome and B-genome chromosomes of polyploid wheat. Here, we report the isolation of a set of disomic substitutions (DS) of S-genome chromosomes for the B-genome chromosomes and their effects on gametophytic and sporophytic development. Ae. speltoides chromosomes were identified by their distinct C-banding and fluorescence in situ hybridization patterns with the Ae. speltoides-derived clone pGc1R-1. Although no large structural differences between S-genome and B-genome chromosomes exist, significant differences in gametophytic compensation were observed for chromosomes 1S, 3S, 5S and 6S. Similarly, chromosomes 1S, 2S, 4S, 5S and 6S affected certain aspects of sporophytic development in relation to spike morphology, fertility and meiotic pairing. The DS5S(5B) had disturbed meiosis with univalents/multivalents and suffered chromosome elimination in the germ tissues leading to haploid spikes in 50% of the plants. The effect of the Ph1 gene on meiosis is well known, and these results provide evidence for the role of Ph1 in the maintenance of polyploid genome integrity. These and other data are discussed in relation to the structural and functional differentiation of S- and B-genome chromosomes and the practical utility of the stocks in wheat improvement.

Role of cytoplasm-specific introgression in the evolution of the polyploid wheats

Studies of N-banded mitotic and meiotic karyotypes of Triticum turgidum L. (2n = 28; AABB) and Triticum timopheevii Zhuk. (2n = 28; AAGG) and hybrids between them, along with observations of meiotic pairing between telocentrics of the AB-genome chromosomes and their respective homologues and homeologues in T. timopheevii, showed that chromosome 4 (m4) of Triticum monococcum L. is present (as 4A(t)) in T. timopheevii but is lacking in T. turgidum. Neither 4A nor 4B pairs with 4A(t), but 4A pairs with 4G and, for this reason and because of its banding pattern, must be considered a B-genome chromosome. T. timopheevii chromosomes 4A(t) and 3A(t) are involved in a reciprocal translocation, and 2A(t), 1G, 2G, and 5G are also involved in translocations. Chromosome arm 4BL occasionally pairs with 7G. The satellites are on the short arms of chromosomes 6A(t) and 6G of T. timopheevii and 1B and 6B of T. turgidum. It is suggested that (i) T. timopheevii orginated as an allotetraploid of Aegilops speltoides Tausch/T. monococcum and (ii) T. turgidum was derived from T. timopheevii by introgressive hybridization with an unknown diploid species, which contributed its distinctive cytoplasm, chromosome 4B or a substantial portion of it, and additional chromosome segments. Rapid fixation of 4B in T. turgidum was ensured by cytoplasm-specific transmission.

Giemsa C-banding and the evolution of wheat

The somatic chromosomes of common wheat, Triticum aestivum L. (2n = 6x = 42), and those of two of its diploid progenitors and T. speltoides, have been individually identified by a Giemsa staining technique. In wheat, telocentric chromosomes were used to aid the recognition of individual chromosomes, and an ideogram has been constructed depicting the C-band positions. There is no similarity in the C-banding of chromosomes within a homoeologous group, with the possible exception of group 5. Comparisons of the C-banding of the diploid species T. monococcum, T. speltoides, and T. tauschii with that of the A, B, and D genomes, respectively, in hexaploid wheat corroborate that T. speltoides could not be the donor of the B genome to wheat and that T. monococcum and T. tauschii are the probable donors of the A and D genomes, respectively.

Fate of Aegilops speltoides-derived, repetitive DNA sequences in diploid Aegilops species, wheat-Aegilops amphiploids and derived chromosome addition lines

The present study reports the cloning and characterization of an Aegilops speltoides-derived subtelomeric repeat, designated as pSp1B16. Clone pSp1B16 has 98% sequence homology with the previously isolated Ae. speltoides repeat Spelt1. The distribution of pSp1B16 and another Ae. speltoides repeat, pGc1R1, was analyzed in diploid Aegilops species, tetra- and hexaploid wheats, wheat-Aegilops amphiploids and derived chromosome addition lines by fluorescence in situ hybridization (FISH). Clones pSp1B16 and pGc1R1 revealed FISH sites in Ae. speltoides, Ae. sharonensis and Triticum timopheevii, whereas additional pGc1R1 FISH sites were observed in Ae. longissima and Ae. caudata. The pSp1B16 and pGc1R1 FISH patterns of the Aegilops chromosomes in the wheat-Aegilops amphiploids and chromosome addition lines are similar to those present in the Aegilops parent accession. We did not observe any evidence of pSp1B16 and pGc1R1 sequence elimination, which is in contrast to previous studies using similar hybrids and repeats. The presented data suggest that the genomic changes in synthetic amphiploids observed in previous studies might be caused by homoeologous recombination, which was suppressed in the amphiploid analyzed in this study.

Molecular cytogenetic characterization of alien introgressions with gene Fhb3 for resistance to Fusarium head blight disease of wheat

Fusarium head blight (FHB) resistance was identified in the alien species Leymus racemosus, and wheat-Leymus introgression lines with FHB resistance were reported previously. Detailed molecular cytogenetic analysis of alien introgressions T01, T09, and T14 and the mapping of Fhb3, a new gene for FHB resistance, are reported here. The introgression line T09 had an unknown wheat-Leymus translocation chromosome. A total of 36 RFLP markers selected from the seven homoeologous groups of wheat were used to characterize T09 and determine the homoeologous relationship of the introgressed Leymus chromosome with wheat. Only short arm markers for group 7 detected Leymus-specific fragments in T09, whereas 7AS-specific RFLP fragments were missing. C-banding and genomic in situ hybridization results indicated that T09 has a compensating Robertsonian translocation T7AL.7Lr#1S involving the long arm of wheat chromosome 7A and the short arm of Leymus chromosome 7Lr#1 substituting for chromosome arm 7AS of wheat. Introgression lines T01 (2n = 44) and T14 (2n = 44) each had two pairs of independent translocation chromosomes. T01 had T4BS.4BL-7Lr#1S + T4BL-7Lr#1S.5Lr#1S. T14 had T6BS.6BL-7Lr#1S + T6BL.5Lr#1S. These translocations were recovered in the progeny of the irradiated line Lr#1 (T5Lr#1S.7Lr#1S). The three translocation lines, T01, T09, and T14, and the disomic addition 7Lr#1 were consistently resistant to FHB in greenhouse point-inoculation experiments, whereas the disomic addition 5Lr#1 was susceptible. The data indicated that at least one novel FHB resistance gene from Leymus, designated Fhb3, resides in the distal region of the short arm of chromosome 7Lr#1, because the resistant translocation lines share a common distal segment of 7Lr#1S. Three PCR-based markers, BE586744-STS, BE404728-STS, and BE586111-STS, specific for 7Lr#1S were developed to expedite marker-assisted selection in breeding programs.

Use of a large-scale Triticeae expressed sequence tag resource to reveal gene expression profiles in hexaploid wheat (Triticum aestivum L.)

The US Wheat Genome Project, funded by the National Science Foundation, developed the first large public Triticeae expressed sequence tag (EST) resource. Altogether, 116,272 ESTs were produced, comprising 100,674 5' ESTs and 15 598 3' ESTs. These ESTs were derived from 42 cDNA libraries, which were created from hexaploid bread wheat (Triticum aestivum L.) and its close relatives, including diploid wheat (T. monococcum L. and Aegilops speltoides L.), tetraploid wheat (T. turgidum L.), and rye (Secale cereale L.), using tissues collected from various stages of plant growth and development and under diverse regimes of abiotic and biotic stress treatments. ESTs were assembled into 18,876 contigs and 23,034 singletons, or 41,910 wheat unigenes. Over 90% of the contigs contained fewer than 10 EST members, implying that the ESTs represented a diverse selection of genes and that genes expressed at low and moderate to high levels were well sampled. Statistical methods were used to study the correlation of gene expression patterns, based on the ESTs clustered in the 1536 contigs that contained at least 10 5' EST members and thus representing the most abundant genes expressed in wheat. Analysis further identified genes in wheat that were significantly upregulated (p < 0.05) in tissues under various abiotic stresses when compared with control tissues. Though the function annotation cannot be assigned for many of these genes, it is likely that they play a role associated with the stress response. This study predicted the possible functionality for 4% of total wheat unigenes, which leaves the remaining 96% with their functional roles and expression patterns largely unknown. Nonetheless, the EST data generated in this project provide a diverse and rich source for gene discovery in wheat.

Advanced backcross QTL analysis of a hard winter wheat x synthetic wheat population

Advanced backcross quantitative trait locus (AB-QTL) analysis was used to identify QTLs for yield and yield components in a backcross population developed from a cross between hard red winter wheat (Triticum aestivum L.) variety Karl 92 and the synthetic wheat line TA 4152-4. Phenotypic data were collected for agronomic traits including heading date, plant height, kernels per spike, kernel weight, tiller number, biomass, harvest index, test weight, grain yield, protein content, and kernel hardness on 190 BC2F(2:4) lines grown in three replications in two Kansas environments. Severity of wheat soil-borne mosaic virus (WSBMV) reaction was evaluated at one location. The population was genotyped using 151 microsatellite markers. Of the ten putative QTLs identified, seven were located on homologous group 2 and group 3 chromosomes. The favorable allele was contributed by cultivated parent Karl 92 at seven QTLs including a major one for WSBMV resistance, and by the synthetic parent at three QTLs: for grain hardness, kernels per spike, and tiller number.

Robertsonian translocations in wheat arise by centric misdivision of univalents at anaphase I and rejoining of broken centromeres during interkinesis of meiosis II

The mechanism of origin of Robertsonian translocations was investigated in plants monosomic for chromosome 1A of wheat and 1H(t) of Elymus trachycaulus by GISH. Chromosomes 1A and 1H(t) stayed univalent in all metaphase I cells analyzed, suggesting that Robertsonian translocations do not originate from meiotic recombination in centromeric regions with shared DNA sequence homology. At ana-/telophase I, the 1H(t) and 1A univalents underwent either chromosome or chromatid segregation and misdivided in 6-7% of the pollen mother cells. None of the ana-/telophases I analyzed had Robertsonian translocations, which were only observed in 2% of the "half tetrads" at ana-/telophase II. The frequency of Robertsonian translocations observed at ana-/telophase II corresponds well with the number of Robertsonian translocations (1-4%) detected in progenies derived from plants monosomic for group-1 chromosomes of wheat (1A, 1B, and 1D) and 1H(t) of E. trachycaulus. Our data suggest that Robertsonian translocations arise from centric misdivision of univalents at ana-/telophase I, followed by segregation of the derived telocentric chromosomes to the same nucleus, and fusion of the broken ends during the ensuing interkinesis.

Inheritance and molecular mapping of new green bug resistance genes in wheat germ plasms derived from Aegilops tauschii

Molecular mapping of genes for crop resistance to the green bug, Schizaphis graminum Rondani, will facilitate selection of green bug resistance in breeding through marker-assisted selection and provide information for map-based gene cloning. In the present study, microsatellite marker and deletion line analyses were used to map green bug resistance genes in five newly identified wheat germ plasms derived from Aegilops tauschii. Our results indicate that the Gb genes in these germ plasms are inherited as single dominant traits. Microsatellite markers X wmc 157 and X gdm 150 flank G bx 1 at 2.7 and 3.3 cM, respectively. Xwmc 671 is proximately linked to G ba, G bb, G bc and G bd at 34.3, 5.4, 13.7, 7.9 cM, respectively. X barc 53 is linked distally to G ba and G bb at 20.7 and 20.2 cM, respectively. X gdm 150 is distal to G bc at 17.9 cM, and X wmc 157 is distal to G bd at 1.9 cM. G bx 1, G ba, G bb, G bc, G bd and the previously characterized G bz are located in the distal 18% region of wheat chromosome 7 DL. G bd appears to be a new green bug resistance gene different from G bx 1 or G bz. G bx 1, G bz G ba, G bb, G bc and G bd are either allelic or linked to Gb 3.

Hessian fly resistance gene H13 is mapped to a distal cluster of resistance genes in chromosome 6DS of wheat

H13 is inherited as a major dominant resistance gene in wheat. It was previously mapped to chromosome 6DL and expresses a high level of antibiosis against Hessian fly (Hf) [Mayetiola destructor (Say)] larvae. The objective of this study was to identify tightly linked molecular markers for marker-assisted selection in wheat breeding and as a starting point toward the map-based cloning of H13. Fifty-two chromosome 6D-specific microsatellite (simple sequence repeat) markers were tested for linkage to H13 using near-isogenic lines Molly (PI 562619) and Newton-207, and a segregating population consisting of 192 F(2:3) families derived from the cross PI 372129 (Dn4) x Molly (H13). Marker Xcfd132 co-segregated with H13, and several other markers were tightly linked to H13 in the distal region of wheat chromosome 6DS. Deletion analysis assigned H13 to a small region closely proximal to the breakpoint of del6DS-6 (FL 0.99). Further evaluation and comparison of the H13-linked markers revealed that the same chromosome region may also contain H23 in KS89WGRC03, an unnamed H gene (H(WGRC4)) in KS89WGRC04, the wheat curl mite resistance gene Cmc4, and a defense response gene Ppo for polyphenol oxidase. Thus, these genes comprise a cluster of arthropod resistance genes. Marker analysis also revealed that a very small intercalary chromosomal segment carrying H13 was transferred from the H13 donor parent to the wheat line Molly.

H9, H10, and H11 compose a cluster of Hessian fly-resistance genes in the distal gene-rich region of wheat chromosome 1AS

H9, H10, and H11 are major dominant resistance genes in wheat, expressing antibiosis against Hessian fly [(Hf) Mayetiola destructor (Say)] larvae. Previously, H9 and H10 were assigned to chromosome 5A and H11 to 1A. The objectives of this study were to identify simple-sequence-repeat (SSR) markers for fine mapping of these genes and for marker-assisted selection in wheat breeding. Contrary to previous results, H9 and H10 did not show linkage with SSR markers on chromosome 5A. Instead, H9, H10, and H11 are linked with SSR markers on the short arm of chromosome 1A. Both H9 and H10 are tightly linked to flanking markers Xbarc263 and Xcfa2153 within a genetic distance of 0.3-0.5 cM. H11 is tightly linked to flanking markers Xcfa2153 and Xbarc263 at genetic distances of 0.3 cM and 1.7 cM. Deletion bin mapping assigned these markers and genes to the distal 14% of chromosome arm 1AS, where another Hf-resistance gene, Hdic (derived from emmer wheat), was also mapped previously. Marker polymorphism results indicated that a small terminal segment of chromosome 1AS containing H9 or H10 was transferred from the donor parent to the wheat lines Iris or Joy, and a small intercalary fragment carrying H11 was transferred from the resistant donor to the wheat line Karen. Our results suggest that H9, H10, H11, Hdic, and the previously identified H9- or H11-linked genes (H3, H5, H6, H12, H14, H15, H16, H17, H19, H28, and H29) may compose a cluster (or family) of Hf-resistance genes in the distal gene-rich region of wheat chromosome 1AS; and H10 most likely is the same gene as H9.

Deletion mapping of homoeologous group 6-specific wheat expressed sequence tags

To localize wheat (Triticum aestivum L.) ESTs on chromosomes, 882 homoeologous group 6-specific ESTs were identified by physically mapping 7965 singletons from 37 cDNA libraries on 146 chromosome, arm, and sub-arm aneuploid and deletion stocks. The 882 ESTs were physically mapped to 25 regions (bins) flanked by 23 deletion breakpoints. Of the 5154 restriction fragments detected by 882 ESTs, 2043 (loci) were localized to group 6 chromosomes and 806 were mapped on other chromosome groups. The number of loci mapped was greatest on chromosome 6B and least on 6D. The 264 ESTs that detected orthologous loci on all three homoeologs using one restriction enzyme were used to construct a consensus physical map. The physical distribution of ESTs was uneven on chromosomes with a tendency toward higher densities in the distal halves of chromosome arms. About 43% of the wheat group 6 ESTs identified rice homologs upon comparisons of genome sequences. Fifty-eight percent of these ESTs were present on rice chromosome 2 and the remaining were on other rice chromosomes. Even within the group 6 bins, rice chromosomal blocks identified by 1-6 wheat ESTs were homologous to up to 11 rice chromosomes. These rice-block contigs were used to resolve the order of wheat ESTs within each bin.

A 2500-locus bin map of wheat homoeologous group 5 provides insights on gene distribution and colinearity with rice

We constructed high-density deletion bin maps of wheat chromosomes 5A, 5B, and 5D, including 2338 loci mapped with 1052 EST probes and 217 previously mapped loci (total 2555 loci). This information was combined to construct a consensus chromosome bin map of group 5 including 24 bins. A relatively higher number of loci were mapped on chromosome 5B (38%) compared to 5A (34%) and 5D (28%). Differences in the levels of polymorphism among the three chromosomes were partially responsible for these differences. A higher number of duplicated loci was found on chromosome 5B (42%). Three times more loci were mapped on the long arms than on the short arms, and a significantly higher number of probes, loci, and duplicated loci were mapped on the distal halves than on the proximal halves of the chromosome arms. Good overall colinearity was observed among the three homoeologous group 5 chromosomes, except for the previously known 5AL/4AL translocation and a putative small pericentric inversion in chromosome 5A. Statistically significant colinearity was observed between low-copy-number ESTs from wheat homoeologous group 5 and rice chromosomes 12 (88 ESTs), 9 (72 ESTs), and 3 (84 ESTs).

A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat

Because of the huge size of the common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) genome of 17,300 Mb, sequencing and mapping of the expressed portion is a logical first step for gene discovery. Here we report mapping of 7104 expressed sequence tag (EST) unigenes by Southern hybridization into a chromosome bin map using a set of wheat aneuploids and deletion stocks. Each EST detected a mean of 4.8 restriction fragments and 2.8 loci. More loci were mapped in the B genome (5774) than in the A (5173) or D (5146) genomes. The EST density was significantly higher for the D genome than for the A or B. In general, EST density increased relative to the physical distance from the centromere. The majority of EST-dense regions are in the distal parts of chromosomes. Most of the agronomically important genes are located in EST-dense regions. The chromosome bin map of ESTs is a unique resource for SNP analysis, comparative mapping, structural and functional analysis, and polyploid evolution, as well as providing a framework for constructing a sequence-ready, BAC-contig map of the wheat genome.

Development and mapping of microsatellite (SSR) markers in wheat

Microsatellite DNA markers are consistently found to be more informative than other classes of markers in hexaploid wheat. The objectives of this research were to develop new primers flanking wheat microsatellites and to position the associated loci on the wheat genome map by genetic linkage mapping in the ITMI W7984 x Opata85 recombinant inbred line (RIL) population and/or by physical mapping with cytogenetic stocks. We observed that the efficiency of marker development could be increased in wheat by creating libraries from sheared rather than enzyme-digested DNA fragments for microsatellite screening, by focusing on microsatellites with the [ATT/TAA]n motif, and by adding an untemplated G-C clamp to the 5'-end of primers. A total of 540 microsatellite-flanking primer pairs were developed, tested, and annotated from random genomic libraries. Primer pairs and associated loci were assigned identifiers prefixed with BARC (the acronym for the USDA-ARS Beltsville Agricultural Research Center) or Xbarc, respectively. A subset of 315 primer sets was used to map 347 loci. One hundred and twenty-five loci were localized by physical mapping alone. Of the 222 loci mapped with the ITMI population, 126 were also physically mapped. Considering all mapped loci, 126, 125, and 96 mapped to the A, B, and D genomes, respectively. Twenty-three of the new loci were positioned in gaps larger than 10 cM in the map based on pre-existing markers, and 14 mapped to the ends of chromosomes. The length of the linkage map was extended by 80.7 cM. Map positions were consistent for 111 of the 126 loci positioned by both genetic and physical mapping. The majority of the 15 discrepancies between genetic and physical mapping involved chromosome group 5.

A chromosome bin map of 2148 expressed sequence tag loci of wheat homoeologous group 7

The objectives of this study were to develop a high-density chromosome bin map of homoeologous group 7 in hexaploid wheat (Triticum aestivum L.), to identify gene distribution in these chromosomes, and to perform comparative studies of wheat with rice and barley. We mapped 2148 loci from 919 EST clones onto group 7 chromosomes of wheat. In the majority of cases the numbers of loci were significantly lower in the centromeric regions and tended to increase in the distal regions. The level of duplicated loci in this group was 24% with most of these loci being localized toward the distal regions. One hundred nineteen EST probes that hybridized to three fragments and mapped to the three group 7 chromosomes were designated landmark probes and were used to construct a consensus homoeologous group 7 map. An additional 49 probes that mapped to 7AS, 7DS, and the ancestral translocated segment involving 7BS also were designated landmarks. Landmark probe orders and comparative maps of wheat, rice, and barley were produced on the basis of corresponding rice BAC/PAC and genetic markers that mapped on chromosomes 6 and 8 of rice. Identification of landmark ESTs and development of consensus maps may provide a framework of conserved coding regions predating the evolution of wheat genomes.

Chromosome bin map of expressed sequence tags in homoeologous group 1 of hexaploid wheat and homoeology with rice and Arabidopsis

A total of 944 expressed sequence tags (ESTs) generated 2212 EST loci mapped to homoeologous group 1 chromosomes in hexaploid wheat (Triticum aestivum L.). EST deletion maps and the consensus map of group 1 chromosomes were constructed to show EST distribution. EST loci were unevenly distributed among chromosomes 1A, 1B, and 1D with 660, 826, and 726, respectively. The number of EST loci was greater on the long arms than on the short arms for all three chromosomes. The distribution of ESTs along chromosome arms was nonrandom with EST clusters occurring in the distal regions of short arms and middle regions of long arms. Duplications of group 1 ESTs in other homoeologous groups occurred at a rate of 35.5%. Seventy-five percent of wheat chromosome 1 ESTs had significant matches with rice sequences (E < or = e(-10)), where large regions of conservation occurred between wheat consensus chromosome 1 and rice chromosome 5 and between the proximal portion of the long arm of wheat consensus chromosome 1 and rice chromosome 10. Only 9.5% of group 1 ESTs showed significant matches to Arabidopsis genome sequences. The results presented are useful for gene mapping and evolutionary and comparative genomics of grasses.

Group 3 chromosome bin maps of wheat and their relationship to rice chromosome 1

The focus of this study was to analyze the content, distribution, and comparative genome relationships of 996 chromosome bin-mapped expressed sequence tags (ESTs) accounting for 2266 restriction fragments (loci) on the homoeologous group 3 chromosomes of hexaploid wheat (Triticum aestivum L.). Of these loci, 634, 884, and 748 were mapped on chromosomes 3A, 3B, and 3D, respectively. The individual chromosome bin maps revealed bins with a high density of mapped ESTs in the distal region and bins of low density in the proximal region of the chromosome arms, with the exception of 3DS and 3DL. These distributions were more localized on the higher-resolution group 3 consensus map with intermediate regions of high-mapped-EST density on both chromosome arms. Gene ontology (GO) classification of mapped ESTs was not significantly different for homoeologous group 3 chromosomes compared to the other groups. A combined analysis of the individual bin maps using 537 of the mapped ESTs revealed rearrangements between the group 3 chromosomes. Approximately 232 (44%) of the consensus mapped ESTs matched sequences on rice chromosome 1 and revealed large- and small-scale differences in gene order. Of the group 3 mapped EST unigenes approximately 21 and 32% matched the Arabidopsis coding regions and proteins, respectively, but no chromosome-level gene order conservation was detected.

Development of an expressed sequence tag (EST) resource for wheat (Triticum aestivum L.): EST generation, unigene analysis, probe selection and bioinformatics for a 16,000-locus bin-delineated map

This report describes the rationale, approaches, organization, and resource development leading to a large-scale deletion bin map of the hexaploid (2n = 6x = 42) wheat genome (Triticum aestivum L.). Accompanying reports in this issue detail results from chromosome bin-mapping of expressed sequence tags (ESTs) representing genes onto the seven homoeologous chromosome groups and a global analysis of the entire mapped wheat EST data set. Among the resources developed were the first extensive public wheat EST collection (113,220 ESTs). Described are protocols for sequencing, sequence processing, EST nomenclature, and the assembly of ESTs into contigs. These contigs plus singletons (unassembled ESTs) were used for selection of distinct sequence motif unigenes. Selected ESTs were rearrayed, validated by 5' and 3' sequencing, and amplified for probing a series of wheat aneuploid and deletion stocks. Images and data for all Southern hybridizations were deposited in databases and were used by the coordinators for each of the seven homoeologous chromosome groups to validate the mapping results. Results from this project have established the foundation for future developments in wheat genomics.

Analysis of expressed sequence tag loci on wheat chromosome group 4

A total of 1918 loci, detected by the hybridization of 938 expressed sequence tag unigenes (ESTs) from 26 Triticeae cDNA libraries, were mapped to wheat (Triticum aestivum L.) homoeologous group 4 chromosomes using a set of deletion, ditelosomic, and nulli-tetrasomic lines. The 1918 EST loci were not distributed uniformly among the three group 4 chromosomes; 41, 28, and 31% mapped to chromosomes 4A, 4B, and 4D, respectively. This pattern is in contrast to the cumulative results of EST mapping in all homoeologous groups, as reported elsewhere, that found the highest proportion of loci mapped to the B genome. Sixty-five percent of these 1918 loci mapped to the long arms of homoeologous group 4 chromosomes, while 35% mapped to the short arms. The distal regions of chromosome arms showed higher numbers of loci than the proximal regions, with the exception of 4DL. This study confirmed the complex structure of chromosome 4A that contains two reciprocal translocations and two inversions, previously identified. An additional inversion in the centromeric region of 4A was revealed. A consensus map for homoeologous group 4 was developed from 119 ESTs unique to group 4. Forty-nine percent of these ESTs were found to be homoeologous to sequences on rice chromosome 3, 12% had matches with sequences on other rice chromosomes, and 39% had no matches with rice sequences at all. Limited homology (only 26 of the 119 consensus ESTs) was found between wheat ESTs on homoeologous group 4 and the Arabidopsis genome. Forty-two percent of the homoeologous group 4 ESTs could be classified into functional categories on the basis of blastX searches against all protein databases.

A 2600-locus chromosome bin map of wheat homoeologous group 2 reveals interstitial gene-rich islands and colinearity with rice

The complex hexaploid wheat genome offers many challenges for genomics research. Expressed sequence tags facilitate the analysis of gene-coding regions and provide a rich source of molecular markers for mapping and comparison with model organisms. The objectives of this study were to construct a high-density EST chromosome bin map of wheat homoeologous group 2 chromosomes to determine the distribution of ESTs, construct a consensus map of group 2 ESTs, investigate synteny, examine patterns of duplication, and assess the colinearity with rice of ESTs assigned to the group 2 consensus bin map. A total of 2600 loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid chromosome and deletion stocks. A consensus map was constructed of 552 ESTs mapping to more than one group 2 chromosome. Regions of high gene density in distal bins and low gene density in proximal bins were found. Two interstitial gene-rich islands flanked by relatively gene-poor regions on both the short and long arms and having good synteny with rice were discovered. The map locations of two ESTs indicated the possible presence of a small pericentric inversion on chromosome 2B. Wheat chromosome group 2 was shown to share syntenous blocks with rice chromosomes 4 and 7.

Lr41, Lr39, and a leaf rust resistance gene from Aegilops cylindrica may be allelic and are located on wheat chromosome 2DS

The leaf rust resistance gene Lr41 in wheat germplasm KS90WGRC10 and a resistance gene in wheat breeding line WX93D246-R-1 were transferred to Triticum aestivum from Aegilops tauschii and Ae. cylindrica, respectively. The leaf rust resistance gene in WX93D246-R-1 was located on wheat chromosome 2D by monosomic analysis. Molecular marker analysis of F(2) plants from non-critical crosses determined that this gene is 11.2 cM distal to marker Xgwm210 on the short arm of 2D. No susceptible plants were detected in a population of 300 F(2) plants from a cross between WX93D246-R-1 and TA 4186 ( Lr39), suggesting that the gene in WX93D246-R-1 is the same as, or closely linked to, Lr39. In addition, no susceptible plants were detected in a population of 180 F(2) plants from the cross between KS90WGRC10 and WX93D246-R-1. The resistance gene in KS90WGRC10, Lr41, was previously reported to be located on wheat chromosome 1D. In this study, no genetic association was found between Lr41 and 51 markers located on chromosome 1D. A population of 110 F(3 )lines from a cross between KS90WGRC10 and TAM 107 was evaluated with polymorphic SSR markers from chromosome 2D and marker Xgdm35 was found to be 1.9 cM proximal to Lr41. When evaluated with diverse isolates of Puccinia triticina, similar reactions were observed on WX93D246-R-1, KS90WGRC10, and TA 4186. The results of mapping, allelism, and race specificity test indicate that these germplasms likely have the same gene for resistance to leaf rust.

Receiver operating characteristic curve analysis of BMI and percentage body fat in type 2 diabetics of Punjab

The present study attempted to establish appropriate cut off levels of Body Mass Index (BMI) for defining overweight as a risk for the development of type 2 diabetes considering percentage body fat (BF) as standard. A total of 300 patients of known type 2 diabetes participated in the study (150 males and 150 females, all > or = 40 years of age). Clinical examination was done. Anthropometric measurements as BMI, Waist Circumference (WC) and Waist-hip ratio (WHR) were calculated. Percentage BF was calculated using skinfold thickness method from the equation of Durnin and Womersley. Mean BMI for males was 24.97 (SD 4.3) kg/m2 and for females was 27.56 (SD 5.14) kg/m2. Mean percentage BF for males was 28.19 (SD 0.74) and for females was 38.22 (SD 5.29). A comparison of BF and BMI data with various ethnic groups revealed conspicuous differences. Receiver operating characteristic (ROC) curve analysis showed a low sensitivity of conventional cut off value of BMI (25 kg/m2) in identifying subjects with overweight as compared to the cut off values based on percentage BF (males > 25, females > 30). This results in substantial misclassification. Based on the ROC curve, a lower cut off value of BMI 22.3 kg/m2, displayed the optimal sensitivity and specificity, and less misclassification in identification of type 2 diabetics with high percentage BF. BF: BMI was calculated and was found to be higher in females.

A strategy for enhancing recombination in proximal regions of chromosomes

As a rule, recombination in bread wheat (Triticum aestivum L.) is low in proximal and high in distal regions of chromosomes. Recombination may be enhanced in proximal regions by using deletion (del) chromosomes deficient for a distal part of a chromosome arm. The chromosome del5BL-11 derived from Chinese Spring (CS) is missing 41% of the distal long arm. This line was made polymorphic by crossing with a stock in which chromosome 5B of CS (5B(CS)) is substituted for chromosome 5B of T. turgidum ssp. dicoccoides origin (5B(T.dic)). Three recombinant del5BL-11 (del5BL-11(rec)) lines were isolated, all resulting from localized recombination between loci Xbcd926 and XksuH1. In del5BL-11(rec), the centromere to fraction length (FL) 0.53 (C-FL0.53) segment is derived from 5B(T. dic) and the distal region of FL 0.55-0.59 is from 5B(CS). Genetic recombination for the C-FL 0.53 interval was assayed in segregating progenies from 5B(CS)/5B(T.dic) and del5BL-11/del5BL-11(rec) crosses using polymorphic markers and for the FL 0.55-0.59 interval in del5BL-11/del5BL-11(rec) cross from chiasma counts. The pairing data and comparative mapping of normal 5B and del5BL-11 indicated that the increase in recombination was restricted to the FL 0.55-0.59 interval of the del5BL-11 chromosome. No significant increase in recombination in more proximal regions was observed although the order of several markers that cosegregated in the normal 5B map was resolved in the del5BL-11 map. The presented data show that recombination in proximal, usually low-recombination, regions can be increased by placing them close to the chromosome end.

Mapping of a resistance gene effective against Karnal bunt pathogen of wheat

A set of 130 wheat recombinant inbred lines (RILs) developed from a cross between parents susceptible (WL711) and resistant (HD29) to Karnal bunt (caused by Tilletia indica), were screened for 3 years with the pathogen populations prevalent in northern India. When 90 simple sequence repeats (SSRs) and 81 amplified fragment length polymorphism (AFLP) loci were mapped on the RILs, markers on chromosomes 2A, 4B and 7B accounted collectively for about one-third of the variation in the disease reaction. The genomic region of largest effect, identified on the long arm of chromosome 4B, reduced Karnal bunt disease by half in three different experiments and accounted for up to 25% of the phenotypic variation for KB reaction. A closely linked SSR marker, GWM538, may be useful in marker-assisted selection for Karnal bunt resistance in wheat.

[RFLP analysis of wheat-L. racemosus translocation lines]

A number of wheat-L. racemosus translocation lines were developed by irradiation, pollen culture and gametocidal chromosome methods. In order to identify homozygous translocation lines and determine the exact location of the breakpoints involved in the translocations, 67 probes genetically or physically mapped previously on wheat chromosomes belonging to seven homoeologous groups were used for RFLP analysis. Three homozygous translocation lines were identified: T1BL.7Lr # 1S, T4BS.4BL-7Lr # 1 and T6AL.7Lr # 1S. In lines T1BL.7Lr # 1S and T6AL.7Lr # 1S, the breakpoint of chromosome 7Lr # 1 was located in the short arm between the area marked by clone MWG808 and that of ABG476.1, and the breakpoints of chromosomes 1B and 6A were both located near the centromere. In line T4BS.4BL-7Lr # 1S, the breakpoint of chromosome 7Lr # 1 was located in the short arm between the area marked by clone BCD349 and that of CDO595, the breakpoint of chromosome 4B was located in the long arm between the area marked by clone CDO541 and that of PSR164.

The centromere structure in Robertsonian wheat-rye translocation chromosomes indicates that centric breakage-fusion can occur at different positions within the primary constriction

Univalent chromosomes at meiotic metaphase I have a tendency to misdivide at the centromeres. Fusion of the misdivision products may produce Robertsonian translocations. The fine structure of the centromeres in Robertsonian wheat-rye translocation chromosomes was analyzed by fluorescence in situ hybridization (FISH) using two centromere-specific DNA clones: pRCS1, derived from rice, and pAWRC1, derived from rye. Clone pRCS1 hybridizes to the centromeres of all grasses including wheat and rye, whereas clone pAWRC1 is rye specific and hybridizes only to the centromeres of rye. Four of the six wheat-rye translocations derived from a single centric misdivision event (1st generation translocations) had hybrid centromeres, with approximately half of the centromere derived from rye and half from wheat. In the two other 1st generation translocations, the entire centromere was derived from rye. Among eight reconstructed wheat and rye chromosomes that originated from two consecutive centric misdivision-fusion events (2nd generation translocations), T1BS.1BL (derived from T1BS.1RL and T1RS.1BL) and one of three T2BS.2BL (derived from T2RS.2BL and T2BS.2RL) had hybrid centromeres. T1RS.1RL (derived from T1BS.1RL and T1RS.1BL), two of three T2BS.2BL, and all three T2RS.2RL (derived from T2RS.2BL and T2BS.2RL) had rye centromeres. All three 3rd generation translocations had hybrid centromeres with approximately half of the centromere derived from rye. There were no indications that the composite structure of the centromere in these chromosomes affected their behavior in mitosis or meiosis. These observations support the notion of a compound structure of the centromere in higher organisms, and indicate that during the centric breakage-fusion event, centromere breakage may occur in different positions along the segment of the chromosome that interacts with the spindle fibers. Normal behavior of the 1st, 2nd, and 3rd generation centric translocations in mitosis and meiosis indicates that, at least in wheat and rye, centromeres are not chromosome specific.