Karyotype and C-Banding Patterns of Mitotic Chromosomes in Diploid Bromegrass (\u3ci\u3eBromus riparius\u3c/i\u3e Rehm)

Previous cytogenetic studies of the genus Bromus L. were limited to chromosome counts and construction of karyotypes on the basis of Feulgen staining. Since the chromosomes of Bromus are similar in morphology, these karyotypes are of limited use for chromosome identification and genome analysis. The objectives of this study were to develop and evaluate a Giemsa C-banding procedure to use in identification of individual bromegrass chromosomes and to develop a karyotype for diploid Bromus riparius Rehm. (2n = 14; PI 440215). All chromosomes had one or more C-bands which were located mainly at telomeric regions. A group (I) of four pairs of chromosomes had telomeric bands on only one arm and could be differentiated. In this group, one pair had an interstitial C-band along with a telomeric band, one pair had a nucleolus organizer region (NOR) at a subtelomeric location on the short arm, and the other two pair could be distinguished by centromere location. The other group (II) of three pairs of chromosomes had telomeric bands on both arms. The unequivocal identification of specific chromosomes of Group II was not possible in all cells because of their similarity and differential condensation of chromosomes. Chromosomes of both groups were either metacentric or submetacentric. The total length of individual chromosomes ranged from 5.58 to 6.87 [micro]m and the arm ratios ranged from 1.02 to 1.5. The homologous chromosomes were paired and assigned numbers I to VII in decreasing length. A karyotype was constructed by means of the C-bands, mean chromosome lengths, and arm ratios. The C-banding procedure used in this study could be used to developed karyotypes for the other species of the genus Bromus and these C-banded karyotypes could be used to compare genomes within the genus

DNA Content and Ploidy Determination of Bromegrass Germplasm Accessions by Flow Cytometry

Species of the genus Bromus represent ploidy states from diploid to decaploid. Ploidy determination of Bromus germplasm is necessary before it can be effectively used in breeding or genetic studies. The objective of this study was to characterize the ploidy of 322 accessions of four Bromus species [Bromus inermis Leyss, B. riparius Rehm, B. biebersteinii Roem and Schult., and B. inermis ssp. pumpellianus (Scribn) Wagnon] that are in the USDA National Plant Germplasm System (NPGS). Flow cytometry was used to determine DNA content of 10 plants of each accession. Mean DNA contents were correlated to ploidy level with root tip chromosome counts on selected accessions whose DNA content indicated that they represented different ploidy levels. On the basis of DNA content (pg [2C.sup.-1] = DNA content of a diploid somatic nucleus) and chromosome counts, mean DNA content and chromosome number was 22.62 pg [2C.sup.-1] for octaploid B. biebersteinii (2n = 8x = 56), 26.07 pg [2C.sup.-1] for decaploid B. biebersteinii (2n = 10x = 70), 11.74 pg [2C.sup.-1] for tetraploid B. inermis (2n = 4x = 28), 22.28 pg [2C.sup.-1] for octaploid B. inermis (2n = 8x = 56), 22.72 pg [2C.sup.-1] for octaploid B. inermis ssp. pumpellianus (2n = 8x = 56), 26.5 pg [2C.sup.-1] for decaploid B. inermis ssp. pumpellianus (2n = 10x = 70), 6.14 pg [2C.sup.-1] for diploid B. riparius (2n = 2x = 14), 22.15 pg [2C.sup.-1] for octaploid B. riparius (2n = 8x = 56), and 26.64 pg [2C.sup.-1] for decaploid B. riparius (2n = 10x = 70). Standard deviations of the mean values were 0.88 pg [2C.sup.-1] or less. Most B. inermis and B. inermis ssp. pumpellianus accessions were octaploid (93.75%), while the majority of the B. riparius and B. biebersteinii were decaploid (92.30%). The B. inermis and related species in the USDA NPGS were collected primarily from areas in the former USSR. The NPGS bromegrass germplasm could be enhanced by collections from western and central Europe, the Middle East, and China

C-Banding Analyses of \u3ci\u3eBromus inermis\u3c/i\u3e Genomes

Smooth bromegrass (Bromus inermis Leyss.) has both tetraploid (2n = 28) and octaploid (2n = 56) ploidy levels that have been difficult to characterize cytogenetically because of similar chromosome morphology. Objectives of this study were to identify individual chromosomes of tetraploid and octaploid B. inermis with C-banding procedures along with chromosome length and arm length ratios, develop more detailed karyotypes than those previously available, and use the karyotypes to examine the genomic relationship of tetraploid and octaploid B. inermis. Root tips of the plants from four tetraploid and three octaploid accessions were used to produce chromosome squash preparations for cytogenetic analysis. The tetraploid B. inermis genome consisted of 12 chromosomes with a telomeric band on each arm and sixteen chromosomes with only one telomeric band on one arm. All of the chromosomes of the tetraploid form, except for four chromosomes, were identified by C-banding patterns, chromosome length, and arm length ratio. The octaploid B. inermis genome consisted of four chromosomes with no C-bands, ≈14 chromosomes with two telomeric bands, and ≈38 chromosomes with only one telomeric band on either the short or long arm. The combined use of C-banding, chromosome size, and arm length ratio only enabled groups of 2, 4, 6, or 8 similar chromosomes to be identified because of similarities in chromosome morphology of the octaploids. Results indicate that tetraploid B. inermis is an allotetraploid since all chromosomes except four could be separated into identifiable pairs. Because of differences between expected and actual numbers of satellite chromosomes and chromosomes with specific C-banding patterns, octaploid B. inermis is probably not a doubled form of the tetraploid B. inermis

Variability of root traits in spring wheat germplasm

Citation: Narayanan S, Mohan A, Gill KS, Prasad PVV (2014) Variability of Root Traits in Spring Wheat Germplasm. PLoS ONE 9(6): e100317. https://doi.org/10.1371/journal.pone.0100317Root traits influence the amount of water and nutrient absorption, and are important for maintaining crop yield under drought conditions. The objectives of this research were to characterize variability of root traits among spring wheat genotypes and determine whether root traits are related to shoot traits (plant height, tiller number per plant, shoot dry weight, and coleoptile length), regions of origin, and market classes. Plants were grown in 150-cm columns for 61 days in a greenhouse under optimal growth conditions. Rooting depth, root dry weight, root: shoot ratio, and shoot traits were determined for 297 genotypes of the germplasm, Cultivated Wheat Collection (CWC). The remaining root traits such as total root length and surface area were measured for a subset of 30 genotypes selected based on rooting depth. Significant genetic variability was observed for root traits among spring wheat genotypes in CWC germplasm or its subset. Genotypes Sonora and Currawa were ranked high, and genotype Vandal was ranked low for most root traits. A positive relationship (R2≥0.35) was found between root and shoot dry weights within the CWC germplasm and between total root surface area and tiller number; total root surface area and shoot dry weight; and total root length and coleoptile length within the subset. No correlations were found between plant height and most root traits within the CWC germplasm or its subset. Region of origin had significant impact on rooting depth in the CWC germplasm. Wheat genotypes collected from Australia, Mediterranean, and west Asia had greater rooting depth than those from south Asia, Latin America, Mexico, and Canada. Soft wheat had greater rooting depth than hard wheat in the CWC germplasm. The genetic variability identified in this research for root traits can be exploited to improve drought tolerance and/or resource capture in wheat

DNA Content and Ploidy Determination of Bromegrass Germplasm Accessions by Flow Cytometry

Species of the genus Bromus represent ploidy states from diploid to decaploid. Ploidy determination of Bromus germplasm is necessary before it can be effectively used in breeding or genetic studies. The objective of this study was to characterize the ploidy of 322 accessions of four Bromus species [Bromus inermis Leyss, B. riparius Rehm, B. biebersteinii Roem and Schult., and B. inermis ssp. pumpellianus (Scribn) Wagnon] that are in the USDA National Plant Germplasm System (NPGS). Flow cytometry was used to determine DNA content of 10 plants of each accession. Mean DNA contents were correlated to ploidy level with root tip chromosome counts on selected accessions whose DNA content indicated that they represented different ploidy levels. On the basis of DNA content (pg [2C.sup.-1] = DNA content of a diploid somatic nucleus) and chromosome counts, mean DNA content and chromosome number was 22.62 pg [2C.sup.-1] for octaploid B. biebersteinii (2n = 8x = 56), 26.07 pg [2C.sup.-1] for decaploid B. biebersteinii (2n = 10x = 70), 11.74 pg [2C.sup.-1] for tetraploid B. inermis (2n = 4x = 28), 22.28 pg [2C.sup.-1] for octaploid B. inermis (2n = 8x = 56), 22.72 pg [2C.sup.-1] for octaploid B. inermis ssp. pumpellianus (2n = 8x = 56), 26.5 pg [2C.sup.-1] for decaploid B. inermis ssp. pumpellianus (2n = 10x = 70), 6.14 pg [2C.sup.-1] for diploid B. riparius (2n = 2x = 14), 22.15 pg [2C.sup.-1] for octaploid B. riparius (2n = 8x = 56), and 26.64 pg [2C.sup.-1] for decaploid B. riparius (2n = 10x = 70). Standard deviations of the mean values were 0.88 pg [2C.sup.-1] or less. Most B. inermis and B. inermis ssp. pumpellianus accessions were octaploid (93.75%), while the majority of the B. riparius and B. biebersteinii were decaploid (92.30%). The B. inermis and related species in the USDA NPGS were collected primarily from areas in the former USSR. The NPGS bromegrass germplasm could be enhanced by collections from western and central Europe, the Middle East, and China

Supplementary File for Capturing wheat phenotypes at the genome level

Supplementary S1: Yield and related traits in bread wheat. Table S1: Examples of genomic regions, candidate and cloned genes for yield and related traits in bread wheat. Supplementary S2: Drought tolerance. Table S2: Examples of genomic regions and candidate genes for drought tolerance. Supplementary S3: Heat tolerance. Table S3. Examples of genomic regions and candidate genes for heat tolerance. Supplementary S4: salinity tolerance in bread wheat. Table S4. Examples of genomic regions and candidate genes for salinity tolerance in bread wheat. Supplementary S5: Frost tolerance. Supplementary S6: Disease resistance. Table S5. Examples of genomic regions, candidate and cloned genes mapped for disease resistance in wheat species. Supplementary S7 insect and mite resistance. Table S6. Examples of genomic regions and candidate genes mapped for insect and mite resistance. Supplementary S8: Quality traits. Table S7. Examples of genomic regions, candidate and cloned genes for quality traits.Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world’s most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public–private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.Peer reviewe

Karyotype and C-Banding Patterns of Mitotic Chromosomes in Diploid Bromegrass (\u3ci\u3eBromus riparius\u3c/i\u3e Rehm)

Previous cytogenetic studies of the genus Bromus L. were limited to chromosome counts and construction of karyotypes on the basis of Feulgen staining. Since the chromosomes of Bromus are similar in morphology, these karyotypes are of limited use for chromosome identification and genome analysis. The objectives of this study were to develop and evaluate a Giemsa C-banding procedure to use in identification of individual bromegrass chromosomes and to develop a karyotype for diploid Bromus riparius Rehm. (2n = 14; PI 440215). All chromosomes had one or more C-bands which were located mainly at telomeric regions. A group (I) of four pairs of chromosomes had telomeric bands on only one arm and could be differentiated. In this group, one pair had an interstitial C-band along with a telomeric band, one pair had a nucleolus organizer region (NOR) at a subtelomeric location on the short arm, and the other two pair could be distinguished by centromere location. The other group (II) of three pairs of chromosomes had telomeric bands on both arms. The unequivocal identification of specific chromosomes of Group II was not possible in all cells because of their similarity and differential condensation of chromosomes. Chromosomes of both groups were either metacentric or submetacentric. The total length of individual chromosomes ranged from 5.58 to 6.87 [micro]m and the arm ratios ranged from 1.02 to 1.5. The homologous chromosomes were paired and assigned numbers I to VII in decreasing length. A karyotype was constructed by means of the C-bands, mean chromosome lengths, and arm ratios. The C-banding procedure used in this study could be used to developed karyotypes for the other species of the genus Bromus and these C-banded karyotypes could be used to compare genomes within the genus