Identification of commercial chicory cultivars for hydroponic forcing and their phenetic relationships revealed by random amplified polymorphic DNAs and amplified fragment length polymorphisms

One‐hundred and twenty‐four amplified fragment length polymorphism (AFLP) and 49 random amplified polymorphic DNA (RAPD) markers have been used to distinguish between 20 and 23 commercial chicory cultivars, respectively. These were all Cichorium intybus var. foliosum F₁ hybrids, currently used in hydroponic forcing. Five‐hundred and twenty RAPD primers (OPERON) were tested, of which 156 resulted in reproducible patterns and 26 yielded polymorphisms. Two‐hundred and fifty‐six AFLP primer‐combinations were tested and six combinations were selected for identification purposes. Similarity indices were measured and clustering has been done using pairwise comparison. Both types of marker provide similar conclusions. Two major clusters are formed, representing late and early cultivars. All cultivars were identified using 10 informative RAPD primers or three AFLP primer combinations. A low degree of polymorphism was detected between some early cultivars, suggesting a narrow genetic base in their breeding strategy.     

利用双杂合位点标记资料构建芒果遗传图谱

为了建立芒果 (MangiferaindicaL )的分子标记遗传图 ,用 15对AFLP (AmplifiedFragmentLengthPolymorphism)引物组合扩增了芒果品种间杂交组合 (Keitt×Tommy Atkins)的 6 0个F1单株 ,获得了 191个多态性位点。它们的分离表现为双杂合 (Aa×Aa)和测交 (Aa×aa)分离两种类型 ,但前者占了 5 9 7%。为了充分利用双杂合位点分离所提供的遗传信息 ,我们根据群体中任意两个双杂合位点隐性个体出现的数目 ,利用二项式分布概率理论推断它们是否连锁以及它们彼此间的相引或相斥关系。在该芒果群体呈 3:1分离的 81个多态性标记中 ,39个被分为 14组 ,以此为基础构建了 15个连锁群 ;这些连锁群共覆盖了 35 4 1cM的芒果基因组。其中 ,最小与最大遗传距离分别为 3 7cM和 2 8 9cM。此外 ,对 18个 1∶1分离类型的标记 ,直接利用Mapmaker作图软件构建了两个芒果连锁群。本文对所提出的利用双杂合位点构建果树遗传图谱的策略进行了讨论。     

Intraspecific olive diversity assessed with AFLP

Amplified fragment length polymorphism (AFLP) was used to study diversity within and among Spanish olive varieties. A high degree of diversity was found among the varieties present in each growing region. Olive oil production and quality relies on appropriate cultivar selection as well as good orchard management. Production based only on a few superior cultivars would result in improved yield, oil quality, and production management. Amplified fragment length polymorphism were evaluated as a tool to identify the intraspecific and intravarietal diversity of olive. Amplified fragment length polymorphism analysis of 38 accessions belonging to 10 cultivars using six primer combinations produced 106 polymorphic bands. Results were analyzed for similarity among accessions via unweighted pair‐group means cluster analysis, resulting in 10 clusters corresponding to named variety designations. Similarity among varieties ranged from 0.60 to 0.72. Diversity within varieties was identified. Similarity within named varieties (accessions with the same varietal name) ranged from 0.75 to 0.96. Differences in several markers were found among 34 accessions. Intravarietal diversity was shown to exist within the Spanish olive varieties grown in the region surrounding Valencia.     

Genetic relationships among species and cultivars of Pistacia using RAPDs and AFLPs

The genus Pistacia (Anacardiaceae) includes 11 species divided into four sections, according to leaf characters and nut morphology. Recently two monophyletic groups have been proposed by using cpDNA,Lentiscus and Terebinthus,containing evergreen and deciduous species, respectively. In the present work molecular markers, derived from two different methods, RAPD and AFLP, are used to study the relationships of native and introducedPistacia species present in Greece. According to the cophenetic correlation coefficients best results for both methods were obtained by using the Jaccard algorithm and the UPGMA clustering method. However, phenograms were constructed using the NJ method (r_cs= 0.987 for RAPDs and r_cs= 0.982 for AFLP), since it is less sensitive against varying mutation rates. Correlation among the genetic similarity (GS) matrices for the two methods was high(r = 0.941). The AFLP and RAPD phenograms were comparable with minor clustering differences. According to our results, two main branches are obtained, one containing the evergreen species P. lentiscusand the resin producing P. lentiscuscv. Chia (cultivated only in the island of Chios), and the other branch containing the deciduous species P. terebinthus,P. palaestina and P. vera, P. chinensis was clustered either with the evergreen species (RAPD data) or with the deciduous species (AFLP data). P. palaestina is clustered to P. terebinthus and can be considered as a subspecies of P. terebinthus, since its GS values are close or smaller than GS values of entries within species (P. vera). The four female cultivars were found to have a narrow genetic basis, probably related to cultivar ‘Nazareth‘ with Syrian origin. This revised version was published online in July 2006 with corrections to the Cover Date.     

Assessment of genetic diversity in selected breeding lines and cultivars of canola quality Brassica juncea and their implications for canola breeding

AFLP markers were used to assess the genetic diversity of 77 breeding lines from three of the world's major canola qualityBrassica juncea breeding programs from Canada (Agriculture and Agri-Food Canada and Saskatchewan Wheat Pool) and Australia (Agriculture Victoria). The objectives of the paper were to assess the genetic diversity within and between these three breeding programs and to assess genetic diversity of the canola quality germplasm as compared to mustard quality B. juncea. Fifteen lines of mustard quality B. juncea from India, China, Russia and Australia were also included in the investigation. Ten EcoR1/Mse1 based primer pairs generated 751 scorable fragments with an average of 26 polymorphic bands per primer pair (35%). Similarity coefficients were calculated using the Simple Matching coefficient and adendrogram was developed using the UPGMA procedure, resulting in germplasm being partitioned into five main groups. Line specific markers were discovered that have potential in enhancing the efficiency of individual breeding programs using breeding techniques like accelerated backcrossing. Further understanding the genetic diversity within and between programs has implications for future breeding and collaboration within and between the three programs. This revised version was published online in July 2006 with corrections to the Cover Date.     

Italian rice varieties: historical data, molecular markers and pedigrees to reveal their genetic relationships

Two molecular marker approaches [amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR)] were employed to study genomic relationship among 96 rice cultivars. These included most of the best reputed Italian accessions. AFLP produced 461 fragments, 248 (53%) of which were polymorphic, SSR produced four to 11 alleles in the 12 genomic loci investigated. Genomic similarity was estimated independently for the two molecular marker techniques. Both AFLP and SSR dendrograms agree in splitting the cultivars into two main clusters: a small one, comprising four exotic accessions, and a larger one which could be split into four subgroups. These were also analysed on the basis of historical and pedigree information. This is the first report on the application of DNA polymorphism analysis to reveal genomic relationship among cultivated Italian rice germplasm. Results will be useful for breeding programmes.     

Genetic diversity estimates in Cicer using AFLP analysis

Amplified fragment length polymorphism (AFLP) analysis was used to evaluate the genetic variation among cultivated chickpea and wild Cicer relatives. In total, 214 marker loci were assessed, of which 211 were polymorphic (98.6%) across the 95 accessions that represented 17 species of Cicer. The genetic variation within a species was highest in C. pinnatifidum followed by C. reticulatum and lowest in C. macracanthum. Three main species groups were identified by UPGMA clustering using Nei's pair‐wise distance calculations. Group I included the cultivated species C. arietinum, C. reticulatum and C. echinospermum. Within this group, C. reticulatum accessions were clustered closest to the C. arietinum cultivars ‘Lasseter’, ‘Kaniva’ and ‘Bumper’, supporting the hypothesis that C. reticulatum is the most probable progenitor of the cultivated species. Cicer bijugum, C. judaicum and C. pinnatifidum were clustered together creating group II. Group III contained all nine perennial species assessed and two annual species C. yamashitae and C. cuneatum. The genetic distance detected between group I and group III (0.13) was equivalent to the genetic distance detected between group I and group II (the primary and annual tertiary species, respectively; 0.14). This indicated that the perennial tertiary species may be as valuable for increasing variation to incorporate novel germplasm in the cultigen as the annual tertiary species.     

Vine-1 retrotransposon-based sequence-specific amplified polymorphism for Vitis vinifera L. genotyping

The sequence‐specific amplification polymorphism (S‐SAP) method, derived from the amplified fragment length polymorphism (AFLP) technique, produces amplified fragments containing retrotransposon long terminal repeat ( LTR ) sequence at one end and a host restriction site at the other. The development and application of this procedure to the LTR of the Vine‐1 element from grapevine is reported. Two primers derived from one of the LTR sequences flanking the retrotransposon were used in combination with MseI degenerated primers on 15 grapevine accessions. S‐SAP results were compared with AFLP data. The heterozygosity and gene diversity values were higher for S‐SAP than for the AFLP procedure. Results show that S‐SAP amplification is effective in identifying polymorphisms and defining genetic distances among cultivars, and could be used for fingerprinting and for ‘Traminer’ clone identification. To the contrary Vine‐1 retrotransposon‐based S‐SAP was not able to distinguish ‘Pinot’ clones.