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PubMed1996

Simple sequence repeats for germplasm analysis and mapping in maize.

Simple sequence repeats (SSRs) are a relatively new class of DNA markers consisting of short runs of tandemly repeated sequence motifs evenly distributed throughout eukaryotic genomes. Owing to the high rate of variation in the number of repeat units, the polymorphism level shown by SSRs is high. Furthermore, they are easy to analyze by means of the polymerase chain reaction, using flanking unique sequence primers. In order to establish the utility of SSR markers for genetic mapping and for the analysis of corn germplasm, corn genomic libraries were constructed and screened for clones containing dinucleotide and trinucleotide repeats. One hundred and fifty clones were isolated and 34 of them were used in this study to analyze 15 (AG)n repeats, 15 (AC)n repeats, and 4 trinucleotide repeats. Twelve corn inbred lines, representing 87% of the RFLP alleles present in a collection of public corn cultivars, were used to assess the information content of the SSR markers. The expected heterozygosity of each SSR marker was compared with the expected heterozygosity of 100 different RFLP markers. The stability of SSRs was also tested through segregation analysis on an existing mapping population.

Alleles↗

PubMed1996

Regional and racial specificities in sorghum germplasm assessed with DNA markers.

Three different molecular marker technologies were used to determine the relatedness of 84 different lines of sorghum. Both racial characterization and geographical origin were found to be correlated with relatedness. In some cases, the region of origin was the more significant factor, where samples of different races from the same locality were more closely related than were samples of the same race from different localities. Wild sorghums were shown to have few novel alleles, suggesting that they would be poor sources of germplasm diversity. The results also indicated that Chinese sorghums are a narrow and distinctive group that is most closely related to race bicolor.

Base Sequence↗

PubMed2006

[Genetic diversity of Dactylis glomerata germplasm resources detected by Inter-simple Sequence Repeats (ISSRS) molecular markers].

Inter-simple Sequence Repeat (ISSR) molecular markers were used to detect the genetic diversity among 50 materials of Dactylis glomerata collected from China and other countries. Twelve primers produced 101 polymorphic bands, averaged 8.41 bands each primer pair. The average percentage of polymorpgic bands was 86.3.8%, and the range of GS (define) was 0.6116-0.9290, indicating a rich genetic diversity of D. glomerata. Based on the cluster and principal component analyses on the genetic characteristics, D. glomerata could be divided into 5 groups according to the nearest phylogenetic relationship. In most cases, accessions from the same continent were classified into the same group, the accessions from China and the United States belong to the different groups, respectively, indicating the geographical distribution of genetic diversity of D. glomerata. The present paper also discussed collection and conservation of germplasm resources in D. glomerata.

Conservation of Natural Resources↗

PubMed2004

ISSR-based clustering of cultivated flax germplasm is statistically correlated to thousand seed mass.

Inter-simple sequence repeat (ISSR)-polymerase chain reaction (PCR) polymorphism was generated to provide useful markers for assessment of genetic diversity within flax germplasm collections. We used nine previously selected anchored ISSR primers for fingerprinting of 53 flax cultivars or genotypes and obtained 62 scorable bands, from which 45 bands (72.6%) were polymorphic. An efficient separation of 53 flax accessions into four groups and eight subgroups was achieved using unweighted pair group method with arithmetic means (UPGMA) clustering procedure based on genetic similarity expressed by the Jaccard similarity coefficient (JSC). Clustering procedure within both groups and subgroups successfully produced smaller homogenous clusters, whereas clustering between the main four groups of flax accessions displayed only a continuous decrease of similarity with a weak clustering effect. Statistical significance of grouping and subgrouping within a cluster dendrogram was estimated by calculation of the error flag and cophenetic correlation parameter for each branch. Principal coordinates (PCO) analysis mostly confirmed the separation by UPGMA clustering. We observed a statistically significant correlation between the number of total vs polymorphic bands in ISSR patterns. A one-way analysis of variance (ANOVA) test confirmed statistically significant differences in the average thousand seed mass (TSM) between eight subclusters of flax accessions from an ISSR-PCR-based UPGMA dendrogram, which indicate statistical correlation between flax ISSR polymorphism (the structure of ISSR-based clustering) TSM.

Cluster Analysis↗

PubMed2002

Evaluation of buffalograss germplasm for resistance to Blissus occiduus (Hemiptera: Lygaeidae).

Blissus occiduus Barber has emerged as an important insect pest of buffalograss, Buchloë dactyloides (Nuttall) Engelmann, in Nebraska. This research evaluated selected buffalograss germplasm for resistance to B. occiduus. Eleven buffalograss selections were screened for chinch bug resistance in three greenhouse studies and two field evaluations. Based on chinch bug damage, NE91-118, 'Tatanka', 'Bonnie Brae', and 'Cody' were rated highly to moderately resistant. These four buffalograsses exhibited minimal damage, even though all were heavily infested with chinch bugs. NE84-45-3 and '378' were highly susceptible to B. occiduus. Field evaluations confirmed chinch bug resistance ratings under field conditions. NE91-118 displayed high levels of resistance in the field screening evaluations, whereas Cody and Tatanka showed moderate levels of resistance, and 378 was highly susceptible.

Animals↗

PubMed2002

Is there meaningful plant resistance to diaprepes abbreviatus (Coleoptera: Curculionidae) in citrus rootstock germplasm?

Host plant resistance to the Diaprepes root weevil, Diaprepes abbreviatus (L.) was assessed for seedlings of 54 Poncirus trifoliata (L.) Raf. selections and two families of progeny from crosses between Citrus and P. trifoliata. Weight gain was consistently lower when larvae were reared in pots containing the progeny of Citrus reticulata Blanco 'Sunki' x P. trifoliata 'Flying Dragon' compared with larvae reared on progeny of 'Pearl' (C. reticulata x C. paradisi Macf.) x 'Flying Dragon'. This is the first evidence of genetic control of resistance to the Diaprepes root weevil within sexually compatible citrus rootstock germplasm. There was a significant positive correlation between percentage root loss and larval weight gain within the resistant progeny, indicating a possible antixenotic effect. Two varieties of P. trifoliata were identified as more resistant than 'Flying Dragon' based on larval weight gain.

Animals↗

PubMed2006

Evaluation of genetic potential of the polyvoltine silkworm (Bombyx mori L.) germplasm and identification of parents for breeding programme.

In the present study, polyvoltine germplasm stock of Andhra Pradesh State Sericulture Research and Development, Institute (APSSRDI) was evaluated for its performance based on quantitative and qualitative traits. Twenty-one oval and 10 peanut cocoon shaped lines were reared in different seasons of the year. Since the polyvoltines are non-diapausing, six generations were reared and evaluated for various economically important traits based on evaluation index and sub-ordinate function statistical methods. Ten top ranked lines obtained by using both the methods were identified as potential parental strains. Among oval lines, APM14, APM11, APM18, APMW9, and APM19, and among peanut lines APMD5, APMD1, APMD3, APMD9 and APMD8 were selected as base material. The identified high yielding lines will be used in various breeding programmes as initial parents for the synthesis of superior polyvoltine breeds/hybrids.

Animals↗

PubMed2002

Comparative Assessment of Variation among Sorghum Germplasm Accessions Using Seed Morphology and RAPD Measurements.

The sorghum germplasm collection currently contains over 42 000 accessions, a number that is too large to manage efficiently. The specific objective of this research was to compare clusters developed from agronomic descriptors with phylogenetic groupings based on random amplified polymorphic DNA (RAPD) fingerprinting of selected sorghum [Sorghum bicolor (L.) Moench] races. Our intent was to identify one approach using agronomic descriptors that would most closely approximate the groupings produced by RAPD markers. Ninety-four accessions of sorghum were grouped into four of the five major races. Differences among accessions determined by various clustering procedures based on agronomic characteristics were compared with clusters developed by means of RAPD markers. Each race varied in the degree of similarity between the four clustering approaches taken and the information provided by RAPD fingerprinting. Test 2, standardization of data by Z-scores and cluster analysis using the complete set of data, provided the highest similarity score for the race bicolor, while Test 3, standardization of data by Z-scores and cluster analysis based on a reduced set of variables selected from principle component analysis, provided the highest similarity scores for the races guinea. Test 1, random selection, was highest for the races caudatum and durra. When averaged over all the races, Test 2 provided the highest similarity score. The results of this study indicate that no one approach to develop clusters by means of agronomic descriptors closely approximate the groupings produced by RAPD markers. These results underscore the need for further research in the evaluation of techniques used to develop core collections and their validity.

Journal Article↗

PubMed1998

Germplasm evaluation in beef cattle-cycle IV: birth and weaning traits.

Gestation length, unassisted calving percentage, perinatal mortality, calf crop weaned (survival from birth to weaning), birth weight, and 200-d weaning weight of 2,597 calves born and 2,433 calves weaned are reported for F1 crosses resulting from matings of Angus, Hereford, Charolais, Gelbvieh, Pinzgauer, Shorthorn, Galloway, Longhorn, Nellore, Piedmontese, and Salers sires to Angus and Hereford dams (> or = 3 yr of age) in Cycle IV of the Germplasm Evaluation (GPE) Program at the U.S. Meat Animal Research Center. Hereford and Angus sires included 1) reference sires born from 1963 to 1971 used in previous cycles of the GPE Program, 2) sires born from 1982 to 1985 (1980s), and 3) sires born from 1983 to 1985 used in natural service clean-up matings. Effects of sire breed of calf were significant for gestation length, unassisted calving percentage, birth weight, and 200-d weaning weight. Gestation length was significantly longer for Nellore than for Charolais, Galloway, Longhorn, Piedmontese, and Salers, which were in turn longer than for Hereford-Angus and Shorthorn. Rankings for birth weight tended to be inversely related to those for calving ease, except for Shorthorn and Salers sires, which required low assistance relative to their heavy birth weights. Rankings for 200-d weight among AI-sired progeny were as follows: Charolais (231.3), Nellore (229.7), Salers (225.5), Shorthorn (223.8), 1980s Hereford-Angus (223.1), Piedmontese (220.0), Galloway (209.5), reference Hereford-Angus (210.1), and Longhorn (199.0); differences > or = 6.5 kg were significant.

Animals↗

PubMed1999

Germplasm evaluation in beef cattle--Cycle IV: postweaning growth and puberty of heifers.

Postweaning growth, puberty, and pregnancy traits were evaluated for 783 F1 heifers sired by Angus, Hereford, Charolais, Shorthorn, Galloway, Longhorn, Nellore, Piedmontese, and Salers bulls and out of Angus and Hereford dams in Cycle IV of the Germplasm Evaluation (GPE) Program at the U.S. Meat Animal Research Center. The Hereford and Angus sires included a sample of bulls born from 1982 to 1985 (1980s HA) as well as reference sires born from 1963 to 1970 (REF HA) used in previous cycles of the GPE program. Breed group of sire had a significant (P<.01) effect on age and weight at puberty, on 200-, 400-, and 550-d weights, on ADG from 200 to 400 and from 400 to 550 d, and 550-d hip height, but it did not influence (P<.05) pregnancy rate. Mean age and weight at puberty were predicted from the cumulative distribution because of censoring of data in each tail of the distribution. Sire breed group rankings (and predicted means in days) for age at puberty were as follows: Piedmontese (332), Shorthorn (338), Charolais (348), REF HA (348), Galloway (351), 1980s HA (352), Salers (355), Longhorn (357), and Nellore (405). Sire breed group rankings (and predicted means in kilograms) for weight at puberty were Longhorn (283), Piedmontese (298), Galloway (305), REF HA (309), Shorthorn (329), 1980s HA (330), Salers (338), Nellore (341), and Charolais (345). Sire breed group rankings (and least squares means in kilograms) for 200-d weight were Charolais (229), Salers (225), Nellore (221), Shorthorn (220), Piedmontese (215), 1980s HA (215), Galloway (209), REF HA (206), and Longhorn (197), with differences >8.3 kg significant. Rankings for 400-d weight (kilograms) were Charolais (390), Shorthorn (384), Salers (380), 1980s HA (374), Nellore (364), REF HA (356), Piedmontese (353), Galloway (348), and Longhorn (321), with differences >11.5 kg significant. Rankings for 550-d weight (kilograms) were Charolais (445), Salers (430), Shorthorn (429), 80's HA (422), Nellore (420), Piedmontese (401), REF HA (398), Galloway (389), and Longhorn (371), with differences >11.7 kg significant. Rankings for 550-d hip height (centimeters) were Nellore (132.2), Charolais (131.9), Salers (129.9), Shorthorn (129.5), Piedmontese (126.7), 1980s HA (126.1), Longhorn (125.3), Galloway (121.7), and REF HA (121.5), with differences >1.35 cm significant. Breed of sire had significant effects on growth and puberty traits of heifers.

Animals↗

PubMed2025

Dissecting adult plant resistance to stem rust through multi-model GWAS in a diverse barley germplasm panel.

INTRODUCTION: Stem rust (SR), caused by Puccinia graminis f. sp. tritici (Pgt), remains a major threat to global barley production, particularly in regions with conducive environments and evolving pathogen populations. Despite progress in understanding seedling resistance, adult plant resistance (APR) to SR remains underexplored in diverse barley germplasm. This study aimed to dissect the genetic architecture of APR to SR in a panel of diverse origins of two-row spring barley using a genome-wide association study (GWAS). METHODS: A total of 273 barley accessions were evaluated for APR to SR in two distinct environments in Kazakhstan. Phenotypic data were combined with high-density SNP genotyping to perform GWAS using five statistical models (GLM, MLM, MLMM, FarmCPU, and BLINK). Population structure and kinship were accounted for to identify robust marker-trait associations (MTAs), followed by haplotype-based QTL delineation. Transcriptomic data from 16 barley tissues were used to identify candidate genes within major QTL regions. Substantial phenotypic variation in SR severity was observed across environments. RESULTS: A total of 204 MTAs were identified, among which 96 were stable across models, resulting in 19 model-stable QTLs spanning all seven barley chromosomes. Six QTLs co-localized with known SR-resistance QTLs and genes, including Rpg1 and Rpg6. Q_rpg_7H.1 (coinciding with Rpg1) was one of the strongest and most consistent QTL, harboring 42 highly expressed candidate genes. A novel major-effect QTL on chromosome 5H, Q_rpg_5H.1 (3.5 - 9.9 Mb), not previously associated with known resistance loci, contained 10 highly expressed genes grouped into three co-expression clusters, including WRKY transcription factors and PR-5 proteins. CONCLUSION: This study provides new insights into the complex, multilayered genetic control of SR resistance in barley. The discovery of both known and novel QTLs offers valuable targets for marker-assisted selection and lays the foundation for breeding durable SR-resistant barley adapted to diverse agroecological conditions.

Hordeum vulgare L.↗

PubMed1999

[Gene analysis of Chinese barley dwarf germplasm resources. I. Inheritance and allelism test of the dwarf genes] [In Process Citation]

The plant height inheritance of 24 Chinese barley dwarf germplasms and the allelic relationships between the dwarf genes in them and the known dwarf genes uz, sdw, br and denso were studied. It was found that most Chinese barley dwarfs were controlled by 1 pair, a few by 2 pairs of recessive genes, only one by 1 pair recessive and 1 pair incomplete dominant genes. Allele frequence at the known dwarf gene uz locus was very high in Chinese barley dwarfs. Most monogenic and 2 digenic barley dwarfs had allelic relationships with uz. A monogenic barley dwarf 11012.2 from India and a digenic dwarf Yan 66 were found allelic to the known dwarf gene sdw. But no dwarfs had allelic relationship with the known dwarf genes br and denso. Monogenic dwarf mutants 91G318, 91D27 and 93-597 carried 1 pair of new recessive dwarf genes respectively. Digenic dwarf mutant 1974E possessed 1 pair of new incomplete dominant dwarf genes. Besides, 4 pairs of new recessive dwarf genes were indentified in 6 Tibetan barley dwarfs.

Journal Article↗

PubMed2000

[Soybean germplasm diversity and genetic variance detected by microsatellite markers].

Microsatellite or Simple Sequence Repeats (SSR) marker is a new type of molecular marker developed recently, which can be used in genotype identification, pedigree analysis, and estimation of genetic distance. Using 5 pairs of SSR primer, 21 polymorphic fragments were obtained in 15 soybean germplasm. The number of alleles at each SSR locus is from 3 to 6, and the range of gene diversity is 0.439-0.668. In addition, analysis of genetic distance was also performed in this study. Pedigree analysis showed that mutation occurred for individuals in the F8 population of RIL after multigeneration meiosis, which was caused because of the changes in the number of repeat unit, to a limited extent.

Alleles↗

PubMedDate not supplied

The use of microsatellite analysis in Solanum tuberosum l. in vitro plantlets derived from cryopreserved germplasm.

This study reports the application of the encapsulation/dehydration cryopreservation and microsatellite analysis to the conservation of Solanum tuberosum cultivars Brodick and Golden Wonder. Cryopreserved shoot-tips were capable of up to 40% shoot and plantlet regeneration in Brodick and >60 % for Golden Wonder. Microsatellite analysis was used with genomic DNA of Golden Wonder and Desiree to establish DNA sequence length polymorphisms. As the basis of stability assessments this technique was applied to: (i) individual, field-grown, plants of Golden Wonder; (ii) individual Golden Wonder plants derived from a single parental tuber progeny; (iii) plantlets derived from in vitro cultures of Golden Wonder and Brodick and (iv) Golden Wonder and Brodick plantlets derived from cryopreserved germplasm

Cryopreservation↗

PubMed2001

[Study on variation and interrelations of characteristics at ginseng germplasms].

The variation and interrelations of some characteristics of Panax ginseng germplasms(lines), which were five selfmating generations of some single plants were studied. Methods of multivariate analysis, such as correlation, regression, or clustering, and coefficient of variation were used. The results were of benefit to the breeding and standardized planting of Panax ginseng.

Genetic Variation↗

PubMed1999

[RAPD analysis of germplasm in "baizhi"].

OBJECTIVE: To analyse the germplasm in Baizhi. METHOD: Using 12 random primers, over seventeen individuals' RAPD were detected in four populations from wild Baizhi (Angelica dahurica), Qi Baizhi and Hang Baizhi. RESULTS: A total of 40 loci were amplified, 26 of which were polymorphism(65%). The PPS values of Hang Baizhi and Qi Baizhi indicate their low levels of genetic diversity. According to the RAPDinstance analysis, the genetic distance(0.16) between Qi Baizhi and Hang Baizhi is shorter than that of the individuals of the populations of Qi Baizhi and Hang Baizhi, and all of these genetic distances are shorter than those between wild Baizhi and Hang Baizhi(Qi Baizhi). CONCLUSION: Hang Baizhi- and Qi Baizhi belong to the same taxon, which is different from the wild Baizhi.

Angelica↗

PubMed2002

[Review of germplasm resources studies on Salvia miltiorrhiza].

Research development of germplasm resources of Salvia miltiorrhiza was reviewed in the aspects of species resource, geographic distribution and varieties, biological characters and culture varieties, and cell and tissue culture. It was suggested that more attention be paid to waters-soluble constituents when evaluating the quality of the medicine, and much more basic studies be done in the course of establishing standard plant base for high quality herb and in the aspect of new variety selection.

Abietanes↗

PubMed2003

[Germplasm characteristics and genetic diversity of Wenchang fowl].

Some germplasm characteristics and genetic diversity of Wenchang fowl produced in tropical/subtropical Hainan were tested, and compared with different ecological types of other chickness. The results showed that the feather colors of Wenchang hens are brown, yellow-brown and yellow-spotted, accounted for 80.83%, while the cocks are mainly red, with some mixed black on their back (71.96%). The crura color of Wenchang fowl was mainly yellow. Its growing velocity was slower, with smaller body weights, body length and crura length at 40 weeks of age, and being obviously of tropical/subtropical ecological characteristics than those of other ecological types. Wenchang fowl was precocious. The egg production rate of the hen at 127 d and 182 d was 5% and 50%, respectively, with an average egg weight of 37.6 +/- 3.2 g. The egg production of hen in 300 d was 73. By DNA-RAPD analysis, the average similarity index of individuals or populations was 0.6071-0.9699 for Wenchang fowl breeds. Thus, Wenchang fowl had a higher homology than other breeds, kept the breed to be pure.

Animals↗