Genetic linkage map construction for white jute (Corchorus capsularis L.) using SRAP,ISSR and RAPD markers

White jute (Corchorus capsularis) and dark jute (Corchorus olitorius) are two important cultivated crops that are used for natural fibre production. Some genetic maps have been developed for dark jute, but the genetic map information for white jute (C. capsularis) is limited. In this study, a linkage map comprising 44 sequence‐related amplified polymorphisms (SRAPs), 57 intersimple sequence repeats (ISSRs) and 18 randomly amplified polymorphic DNA (RAPD) covering 2185.7 cM with a mean density of 18.7 cM per locus was constructed in an F₂ population consisting of 185 individuals derived from a cross between two diverse genotypes of ‘Xinxuan No. 1’ and ‘Qiongyueqing’ in white jute. These markers were evenly distributed in the linkage groups without any clustering. This genetic linkage map construction will facilitate the mapping of agronomic traits and marker‐assisted selection breeding in white jute.     

Genetic diversity in soybean genotypes from north‐eastern China and identification of candidate markers associated with maturity rating

Random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers were used to estimate the genetic relationships among 101 soybean cultivars developed in north‐eastern China. Fifty‐three fragments of the 100 RAPD markers and 35 SSR markers tested were polymorphic across the 101 soybean cultivars. Similarity values among these soybean cultivars ranged from 45.2% to 100% for RAPD data, and ranged from 36.1% to 100% for SSR data. The similarity matrices for SSR data and RAPD data were moderately correlated (r = 0.31, P < 0.05). Cluster analyses indicated that the cultivars released from the same seed company were mostly grouped together. A principal component analysis, based on the combined RAPD and SSR data, yielded a good separation of soybean varieties with different maturity ratings [represented by soybean Heat Unit (HU)]. The varieties with HU < 2200 were well separated from those with HU > 2200. Four RAPD markers and eight SSR markers were significantly associated with the maturity ratings of soybean.     

A genetic diversity analysis of wild Lespedeza populations based on morphological characters, allozyme and RAPD methods

Genetic variability within and among 14 Chinese natural populations of Lespedeza Michx. Used mainly for wildlife food and cover and for erosion control was evaluated on the basis of morphological characteristics, allozyme markers and random amplified polymorphic DNAs (RAPDs). All methods disclosed a high degree of allelic heterogeneity among samples, also revealing a high degree of gene diversity. Genetic variation among populations was higher for RAPD than for enzyme loci. Correlation between morphological, allozyme and RAPD distance matrices were calculated by Mantel’ tests. There was a little disparity between the three level's distances on population relationships. However, there is a weak significant correlation (P < 0.001) between morphology and allozyme distances as well as morphology and RAPD distances, and the test of this correlation is very high.     

Genetic diversity of hexaploid wheat cultivars estimated by RAPD markers, morphological traits and coefficients of parentage

Estimates of genetic diversity can be based on different types of data. The aim of this research were to study genetic diversity among Croatian wheat cultivars by random amplified polymorphic DNA (RAPD) markers, morphological traits and pedigree records; to analyse differences between wheat cultivars from two breeding centres; and to evaluate usability of RAPD markers for estimation of genetic diversity among wheat cultivars in comparison with morphological traits and pedigree record data. Studies were conducted on 14 wheat cultivars and breeding lines from two breeding centres in Croatia. For the RAPD analysis 36 primers were screened and the 14 most polymorphic ones yielded 341 polymorphic bands. Twelve morphological traits were used for morphological analysis. Pedigrees were composed of seven generations of ancestors. RAPD markers showed a high level of polymorphism among the cultivars examined and the breeding lines. No significant correlations were observed among the methods tested.     

黄麻全基因组SSR鉴定与特征分析

黄麻是世界上重要的天然韧皮部纤维作物之一。然而, SSR标记的缺乏限制了黄麻的遗传改良。本研究从圆果种黄麻测序品种CVL-1的基因组、基因、CDS和cDNA中挖掘SSR信息,利用SSR Primer软件查找SSR位点,并分析其分布特征。结果表明,基于基因组序列共开发了153,242个基因组SSR,平均密度为467.20个SSRMb~(–1);基于cDNA序列开发了10,747个SSR,平均密度为260.85 SSR Mb~(–1)。大部分重复基元为二至四核苷酸,占76.91%,其中cDNA序列SSR中三核苷酸重复基元数量较多而基因组SSR中二核苷酸重复基元数量较多。对于不同类型的SSR重复基元,随着重复单元数量的增加,其基因组和cDNA的SSR分布频率呈现逐步降低特征。黄麻全基因组SSR标记鉴定,不仅可以丰富黄麻分子标记的数量,而且为剖析黄麻重要农艺性状的遗传机制奠定基础。     

Evaluation of newly developed SSR markers and identification of quantitative trait loci for bast fibre cellulose in white jute (Corchorus capsularis)

Cellulose is one of the main chemical component of bast fibre in jute. However, quantitative trait loci (QTL) for bast fibre cellulose content remains elusive. In this study, we identified 846 new SSR markers from 70,792 unigenes in the NCBI and validated them in a panel of 24 diverse jute accessions. Of 846 SSRs, 748 (88.41%) were successfully amplified, and 585 (69.14%) showed polymorphisms, implying that these are high‐quality SSRs. Furthermore, 585 SSRs along with 5,074 polymorphic SLAF (specific locus amplified fragment) and 173 InDel markers were used to reconstruct a high‐dense linkage map in a recombinant inbred population with 104 F₈ lines. Totally, 835 markers were successfully mapped to a whole length of 604.5 cM with a mean distance of 2.84 cM between adjacent markers. Furthermore, five QTLs for bast fibre cellulose were identified. One major QTL (qBFC1‐1) was stable in 2 years and explained average phenotypic variance with 14.34%. These results may be useful for developing enhanced bast fibre quality in white jute through marker‐assisted selection (MAS) breeding.     

Genetic diversity among populations and breeding lines from recurrent selection in Brassica napus as revealed by RAPD markers

Recurrent selection facilitated by dominant male sterility has been conducted to broaden the genetic basis for cultivar development in Brassica napus. This study aimed to evaluate the genetic variation in four base populations (C0‐C3) and breeding lines from two of the populations produced during recurrent selection by random amplified polymorphic DNA (Rapd) markers. Genetic variation in four populations declined gradually with the advance of selection cycles as measured by expected genetic heterozygosity (from 0.2058 in C0 to 0.1536 in C3) but the decline was not statistically significant. When compared with the average genetic distances for 21 germplasm collections with wide geographical and genetic origins (0.4712) and seven breeding lines from pedigree selection (0.2059), seven breeding lines selected from the C1 population and 11 from the C3 population had a larger average genetic distance (0.5339 and 0.5486, respectively). Clustering analysis indicated that the lines from recurrent selection had a much lower genetic similarity than lines from pedigree selection. Our results suggest that base populations derived from recurrent selection could provide a wider genetic variation for selection of breeding lines with more broad genetic bases.     

Sex-linked SSR markers in hemp

Hemp is a dioecious plant with sex chromosomes X and Y, the male sex being heterogametic. The quality of the fibre depends on the sex type. The sex chromosomes can be characterized by molecular markers. In this report, sex‐linked simple sequence repeat (SSR) markers are described. One SSR marker was polymorphic in both the populations derived from single crosses, two other markers in but one of the two populations. Three alleles were detected for two SSR markers indicating polymorphism not only between X and Y, but also between different X chromosomes. In addition, several sex‐linked RAPD markers were detected in one population. Recombination within the sex chromosomes was observed for nearly all markers.     

Bringing wild relatives back into the family: recovering genetic diversity in CIMMYT improved wheat germplasm

Summary The dangers of a narrow genetic base of the world's major domesticated food crops have become a great global concern in recent decades. The efforts of the International Maize and Wheat Improvement Center (CIMMYT) to breed common wheat cultivars for resource poor farmers in the developing world (known as the Green Revolution wheats) has met with notable success in terms of improved yield, yield stability, increased disease resistance and utilization efficiency of agricultural inputs. However, much of the success was bought at the cost of an overall reduction in genetic diversity in the species; average Modified Roger's distances (MRD) within groups of germplasm fell from 0.64 in the landraces to a low of 0.58 in the improved lines in the 1980s. Recent efforts by CIMMYT breeders to expand the genetic base of common wheat has included the use of landraces, materials from other breeding programs, and synthetic wheats derived from wild species in the pedigrees of new advanced materials. The result, measured using SSR molecular markers, is a highly significant increase in the latent genetic diversity of recently developed CIMMYT breeding lines and cultivars compared to the original Green Revolution wheats (average MRD of the latest materials (0.63) is not significantly different from that of the landraces, as tested using confidence intervals). At the same time, yield and resistance to biotic and abiotic stresses, and end-use quality continue to increase, indicating that the Green Revolution continues to this day.     

Identification of molecular markers associated with oleic and linolenic acid in spring oilseed rape (Brassica napus)

The quality of the oil derived from oilseed rape is determined by its fatty acid composition. Breeding oilseed rape for enhanced oil quality includes the development of cultivars with high oleic and low linolenic acid. Random amplified polymorphic DNA (RAPD) and intersimple sequence repeat (ISSR) techniques were investigated for the development of molecular markers for genes controlling oleic and/or linolenic acid. Markers that were identified were converted to sequence characterized amplified region (SCAR) markers for use in breeding. Molecular markers associated with these two fatty acids were identified in a doubled haploid population derived from a cross between the oilseed rape lines TO99‐5318‐20, very high oleic (>79%) and very low linolenic acid (<2%) × DH12075, high oleic (68%) and higher linolenic acid (>7%). Eight RAPD markers were associated with oleic and linolenic acid contents. The RAPD marker UBC 2₈₃₀ accounted for 43% and 13% of the genetic variation for oleic and linolenic acid levels, respectively. The RAPD marker UBC 153₅₅₀ accounted for 19% of the genetic variation for linolenic acid. The UBC 2₈₃₀ fragment was converted to a SCAR marker. The markers identified in this study should be useful tools for the early generation selection of high oleic and low linolenic acid genotypes in oilseed rape breeding programmes.     

Genetic diversity among tea cultivars from China, Japan and Kenya revealed by ISSR markers and its implication for parental selection in tea breeding programmes

Tea plant [Camellia sinensis (L.) O. Kuntze] is an important beverage crop in the world. In recent years many clonal tea cultivars have been released, and they play major roles in improving the production and quality of tea. It is important to understand the genetic diversity and relatedness of these cultivars to avoid inbreeding and narrow genetic basis in future tea breeding. In the present study, genetic diversity and relationship of 48 tea cultivars from China, Japan and Kenya were evaluated by inter‐simple sequence repeat (ISSR) markers. A total of 382 ISSR bands were scored, of which 381 (99.7%) were polymorphic. The ISSR primers showed high ability to distinguish between tea cultivars according to their high Resolving Power (R_P) with an average of 7.4. The mean of Nei’s gene diversity (H) and Shannon’s information index (I) were 0.22 and 0.35, respectively. More abundant diversity was revealed among cultivars in China than those in Japan and Kenya. Within Chinese populations, the level of diversity in east China was higher than that in other regions. The coefficient of genetic differentiation (G_ST) was 0.202, which indicates a high degree of genetic variation within populations. This result was further confirmed by analysis of molecular variance, which revealed the variance component within the populations (92.07%) was obviously larger than that among populations (7.93%). The level of gene flow (N_m) was estimated to be 2.0. This could be explained by frequent natural cross‐pollination and seed dispersal among tea populations. The pairwise similarity coefficient between the cultivars varied from 0.162 to 0.538. A dendrogram of 48 tea cultivars was constructed where all the tested cultivars were divided into two groups. Our data show that the genetic relationship among tea cultivars can be determined by the ISSR markers. This will provide valuable information to assist parental selection in current and future tea breeding programmes.     

AFLP, ISSR and RAPD markers reveal high levels of genetic diversity among Lupinus spp.

The Lupinus genus includes a number of important crop species. The use of defined nucleotide sequences for the analysis of genetic diversity among these species has revealed modest levels of diversity. The aim of this study was to access AFLP, ISSR and RAPD markers to evaluate the genetic diversity among L. albus, L. angustifolius, L. cosentinii, L. hispanicus, L. luteus, L. mutabilis, L. pilosus and L. polyphyllus. Unexpectedly, low levels of genetic similarity were found (ranging from 0.205 to 0.432), regardless of the type of molecular marker used. Nevertheless, these techniques consistently showed a greater genetic similarity between L. pilosus and L. cosentinii, L. mutabilis and L. polyphyllus and among L. luteus, L. hispanicus and L. angustifolius, clearly separating the Old World from the New World species. Such low genetic similarity among Lupinus spp. is most unlikely to be due to differences in coding sequences but could be the result of a long diverging process concerning non‐coding regions, which would represent a very important proportion of these genomes.     

Evaluation of the genetic diversity among elite tea (Camellia sinensis var. sinensis) accessions using RAPD markers

The diversity of 27 superior tea (Camellia sinensis var. sinensis) accessions from Korea, Japan and Taiwan was examined with RAPD-PCR (Random Amplified Polymorphic DNA Polymerase Chain Reaction) markers. Out of the 50 primers screened, 17 primers generated 58 polymorphic and reproducible bands. A minimum of 3 primers was sufficient to distinguish all the 27 accessions studied. The Shannon's index used to partition diversity into inter- and intra-group, revealed that 71 percent of variability resided within groups and 29 percent between groups. Diversity was greatest within the Korean group followed by Taiwan and Japan. The relatively high diversity observed in Korea might reflect the larger genetic base of its plantations while the low diversity in Japan could be explained by the long and intensive tea selection programme in this country. A dendrogram based on the UPGMA-link method using Jaccard's distances and multivariate Factorial correspondence analysis clustered the tea accessions into two main groups, regrouping the Taiwan cultivars on the one side and the Korean and Japanese accessions on the other side. This suggests that the Taiwan tea studied here may have a different origin from that of Korea and Japan. This revised version was published online in July 2006 with corrections to the Cover Date.     

Identification of RAPD markers for resistance to coffee berry disease, Colletotrichum kahawae, in arabica coffee

Resistance to Coffee Berry Disease (CBD) in Arabica coffee is controlled by at least three genes which are present in the varieties Hibrido de Timor (T gene), Catimor (T gene), Rume Sudan (R and k genes) and K7 (k gene). Hibrido de Timor, Catimor and Rume Sudan are genetically distant from most of the commercial cultivars, and the utilisation of molecular markers would greatly improve the efficiency of breeding programmes concerned with CBD resistance. The objectives of the present work were therefore: (1) to identify random amplified polymorphic DNA (RAPD) markers associated with CBD resistance and (2) to identify markers which could be used to select against the genetic background of the resistance donors. Identification of RAPD markers was carried out in three steps. The first step involved the comparison of the RAPD profiles between the susceptible cultivars and the resistant donors. This was followed by comparison of the RAPD profiles between resistant and susceptible types of each donor variety. The final step involved assay of the resistance markers in the first and the second backcrosses between these donors and the recurrent parent. High genetic variability was demonstrated in Catimor, and to some extent in Rume Sudan. Three RAPD markers were shown to be closely associated to the T gene. Attempts to identify markers associated with the R and k genes were less rewarding. The implications of the current observations in relation to breeding for CBD resistance in Arabica coffee are discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic diversity and differentiation of Chinese wild soybean germplasm (G. soja Sieb. & Zucc.) in geographical scale revealed by SSR markers

Wild soybean (Glycine soja), as the progenitor of soybeans (G. max), is widely distributed in China and has been collected as a supplementary germplasm pool of soybeans. In this study, 375 wild soybean accessions from a set of genebank core collection were analysed for genetic diversity by using 42 simple sequence repeat primer pairs. The mean allele number per locus was 19.62. Ten‐percent unique alleles involving 35 or 83.33% loci differentiated among the geographical regions. The mean gene diversity (h) per locus was 0.89. A very low mean coefficient of gene differentiation (G_ST = 0.08) for geographical regions and a high mean within‐region gene diversity (H_S = 0.81) were observed, indicating that most genetic diversity existed within the regions. There was an obvious relationship between genetic distance and geographical distance. The results showed multiple centers of genetic diversity for Chinese wild soybean in North China, the Huanghe River Valley, and Central China as well as the Changjiang River Valley, implicating multiple site origins of soybeans within China.     

Development of RAPD markers associated with common bunt resistance to race T1 (Tilletia tritici) in spelt wheat

Common bunt caused by Tilletia tritici and T. laevis has occurred worldwide and reduces yield and quality in common and durum wheats. The development of DNA markers linked to bunt resistance to race T1 in the cross, ‘Laura’(S) בRL5407’ (R), was carried out in this study based on the single head derived F_4:5 and single seed derived F_4:6 populations. Bulked segregant analysis was used to identify two random amplified polymorphic DNA (RAPD) markers linked to the gene for resistance to race T1 in the spelt wheat ‘RL5407′. The two markers identified, UBC548₅₉₀ and UBC274₉₈₈, flanked the resistance gene with a map distance of 9.1 and 18.2 cM, respectively. The former was linked in repulsion phase to bunt resistance while the later was in coupling phase. The two RAPD markers and the common bunt‐resistance gene all segregated in Mendelian fashion. Use of these two RAPD markers together could assist in incorporating the bunt‐resistance gene from spelt wheat into common wheat cultivars by means of marker‐assisted selection.     

Development of EST‐SSR markers for diversity and breeding studies in opium poppy

All publicly available opium poppy expressed sequence tag (EST) sequences, totalling 20 885, were assembled into unigenes and examined for simple sequence repeats (SSRs). Nearly 19% of the 14 957 unigenes contained SSRs with 4% harbouring more than one SSR. Average density of the SSRs was 1 SSR per 3.6 kb of non‐redundant EST sequence. Trinucleotide SSRs were most frequently identified (39%), and many of the most prevalent motifs were AT‐rich. Flanking primers were designed for 86% of the SSRs and 67 primer pairs were tested on 37 opium poppy accessions and seven related species. All markers were transferable to the related species. Polymorphism information content (PIC) values for the markers were intermediate for comparisons within opium poppy (average of 0.27) and slightly higher for comparisons across species (average of 0.29). The markers were found to be useful for diversity analysis as they successfully distinguished among Turkish opium poppy accessions and land races.