Breeding potential of Belgian landraces of leek ( Allium ampeloprasum L. var. porrum)

Western Europe is the world's greatest leek producing and consuming region. Belgium is situated in the centre of Western Europe and can be considered as a genepool of landraces of leek. Although the commercial varieties nowadays take over the successes of Belgian landraces, this paper deals with the breeding potential of the Belgian landraces. Typing the Belgian landraces was done in an observation trial together with 50 cultivars. Clustering analysis revealed that 4 of the Belgian landraces were autumn types, 2 landraces were of the early winter type and another 12 landraces were ranged with 6 commercial varieties to form the most winterhardy group of leek. For the important characteristics leaf colour and senescence resistance, the Belgian landraces were better than most of the commercial varieties. Although, for economically more important characteristics shaft length and some disease resistance they scored low. Finally, in this trial, the Belgian landraces were high yielding, especially in the late season. But also in the early season (harvest in September and November) some Belgian landraces were in the top 10 for yield. At harvest in February 9 of the 10 best yielding winterleeks were Belgian landraces. This proves that the Belgian landraces were well adapted to the soil and climate of this region. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic linkage map of cassava (Manihot esculenta Crantz) based on AFLP and SSR markers

To generate a genetic linkage map of cassava ( Manihot esculenta Crantz), 58 F₁ progenies from a cross between Rayong 90 (female) and Rayong 5 (male) were examined in amplification fragment length polymorphism (AFLP) and simple sequence repeat (SSR) analyses. A total of 469 polymorphic markers consisting of 378 AFLPs generated from 76 primer combinations and 91 SSRs were identified. These markers were analyzed using the joinmap ^® 3.0 package program to construct a genetic linkage map. A total of 33 linkage groups of a common map were constructed from 119 AFLPs and 18 SSRs, spanning 1095 cM with an average of 7.99 cM between markers. The genetic linkage map generated in this study will be useful for genetic studies in cassava particularly for the identification of genetic markers linked to traits of interest, although the complex cassava genome suggests that maybe a long term objective.     

The causes and consequences of meiotic irregularity in the leek (Allium ampeloprasum spp. porrum); implications for fertility, quality and uniformity

We have previously confirmed that Allium ampeloprasum spp. porrum, the leek, shows extensive and frequent quadrivalent formation during prophase I of meiosis, and that despite the resolution of most of these into bivalents some quadrivalents persist to metaphase I; in addition, a substantial number of univalents are found at this stage. In this paper we examine the later meiotic and post meiotic consequences of these irregularities in four leek cultivars and discuss their implications. Irregularities of chromosome segregation are observed at anaphase of both meiotic divisions, giving rise to micronuclei in dyad and tetrad stage pollen mother cells. It is shown that micronucleus frequency in tetrads is correlated with univalent frequency at metaphase I, suggesting that micronuclei originate largely from missegregation of univalents. Seedling populations of the same four cultivars were screened cytologically and shown to contain aneuploids at frequencies ranging between 4.3% and 8.4%. It is proposed that the majority of aneuploid seedlings originate from meiotic irregularity, especially univalent missegregation. It is very likely that the presence of this level of aneuploidy in the seedling populations contributes to the problems of phenotypic non-uniformity experienced by the leek crop, although its relative importance is difficult to assess. Further studies are required to establish the genetical and environmental contributions to meiotic irregularity and to assess the potential for selection for greater meiotic regularity in this material. This revised version was published online in July 2006 with corrections to the Cover Date.     

An AFLP-based linkage map of Zoysiagrass (Zoysia japonica)

To construct an amplified‐fragment length polymorphism (AFLP)‐based molecular linkage map of zoysiagrass, the selfed progenies of a clone consisting of 78 individuals were analysed using 471 AFLP markers derived from 126 PstI/MseI primer combinations. Of these markers, 364 were grouped into 26 linkage groups. The maps covered a total length of 932.5 cM, with an average spacing of 2.6 cM between markers. This information proves useful for gene targeting, quantitative trait loci mapping, and marker‐assisted selection in zoysiagrass.     

Clustering of amplified fragment length polymorphism markers in a linkage map of rye

Amplified fragment length polymorphisms (AFLPs) are now widely used in DNA fingerprinting and genetic diversity studies, the construction of dense genetic maps and in fine mapping of agronomically important traits. The AFLP markers have been chosen as a source to extend and saturate a linkage map of rye, which has previously been generated by means of restriction fragment length polymorphism, random amplified polymorphic DNA, simple sequence repeat and isozyme markers. Gaps between linkage groups, which were known to be part of chromosome 2R, have been closed, thus allowing the determination of their correct order. Eighteen EcoRI‐MseI primer combinations were screened for polymorphism and yielded 148 polymorphic bands out of a total of 1180. The level of polymorphism among the different primer combinations varied from 5.7% to 33.3%. Eight primer combinations, which revealed most polymorphisms, were further analysed in all individuals of the F₂ mapping population. Seventy‐one out of 80 polymorphic loci could be integrated into the linkage map, thereby increasing the total number of markers to 182. However, 46% of the mapped AFLP markers constituted four major clusters located on chromosomes 2R, 5R and 7R, predominantly in proximity to the centromere. The integration of AFLP markers caused an increase of 215 cM, which resulted in a total map length of almost 1100 cM.     

Antioxidant changes during postharvest processing and storage of leek (Allium ampeloprasum var. porrum)

The evaluation of the impact of postharvest processing and storage on the health benefits of vegetables is of great practical importance. Reports on their effect on the antioxidant capacity, polyphenol and S-alk(en)yl-l-cysteine sulfoxide (ACSO) content, i.e. isoalliin and methiin of the white shaft of leek (Allium ampeloprasum var. porrum), however, are limited. This study determined the levels of the antioxidant properties of leek from postharvest processing at the farm until refrigerated storage of 13 days at the consumer. Two cases were investigated, (1) leek sold as an entire plant and (2) leek with a large part of the green leaves removed, where the shafts are sold in a plastic package. The antioxidant capacity and the total content of phenolic compounds in the white shaft of the entire and packaged leek was stable during 13 days of refrigerated storage. A significant increase in the concentration of isoalliin was observed. Comparing the entire and processed/packaged leek, significant differences could be observed in antioxidant properties. The ACSO content in the white shaft of packaged leek was significant lower than the content in the white part of the entire leek. Therefore, the minimal processing step of cutting the green leaves and roots had an influence on the levels of antioxidant properties.     

Inbreeding depression and single cross hybrids in leeks (Allium ampeloprasum ssp. porrum)

Summary All current commercial cultivars of leeks are open-pollinated and one of the major problems with the crop is poor uniformity with much of the variation being genetic in origin. Inbred lines and single cross hybrids were produced to try to reduce the genetic variation. Inbreds were generated by single seed descent from 5400 plants taken from six commercial cultivars and performance data for uniformity, yield and quality are presented for the S₁-S₃ generations. A few relatively vigorous inbred lines were obtained but overall, inbreeding depression was very severe with no compensating increase in uniformity as measured by coefficients of variation. In contrast, the experimental hybrids gave significant uniformity, yield and quality benefits compared to open-pollinated commercial cultivars and can be used as the basis for developing a range of commercial hybrid cultivars.Abbreviations SSD Single Seed Descent - HRI Horticulture Research International     

Causal relationships between inbreeding, seed characteristics and plant performance in leek (Allium porrum L.)

Leek (Allium porrum L.) is an important outdoor vegetable in West Europe, where it is cultivated on about 30,000 ha. Most commercial cultivars of leek are open pollinated. One of the major problems with the crop is poor uniformity. Leek is an outbreeding species with up to 20% self-fertilisation. Much of the variation of open pollinated cultivars is explained by the strong sensitivity to in breeding depression after selfing. In this study we attempt to analyse in a systematic way the relationship between degree of selfing and agricultural performance in leek. The results obtained confirm a negative correlation between selfing and somea gricultural aspects important for vigour such as seedling emergence, plant growth and plant fresh yield. Also negative correlations between degree of selfing and seed individual weight and between selfing and seed individual size were found. The negative relationship between inbreeding and plant weight at harvest is further confirmed in an experiment in which the origin (cross-pollination orself-pollination) of each individual offspring plant analysed was determined using AFLP-markers. Finally, the correlation between chlorophyll deficiency genes and the loss of vigour that follows selfing was investigated. The results obtained demonstrate a significant decrease of pigment content in two generations of selfing. This revised version was published online in July 2006 with corrections to the Cover Date.     

Cultivar identification and genetic map of mango (Mangifera indica)

Amplified Fragment Length Polymorphism (AFLP) information was used for identification of mango (Mangifera indica L.) cultivars, for studying the genetic relationship among 16 mango cultivars and seven mango rootstocks and for the construction of a genetic linkage map. Six AFLP primer combinations produced 204 clear bands and on the average 34 bands for each combination. The average Band-Sharing between cultivars and rootstocks was 83% and 80%, respectively. The average Band-Sharing for mango is 81%. The probability of obtaining a similar pattern for two different mango cultivars and rootstocks is 6 × 10⁻³and 2 × 10⁻³, respectively. A preliminary genetic linkage map of the mango genome was constructed, based on the progeny of a cross between ‘Keitt’ and ‘Tommy-Atkins’. This linkage map consists of 13 linkage groups and covers 161.5 cm defined by 34 AFLP markers. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic mapping of AFLP markers in Japanese bunching onion (<Emphasis Type="Italic">Allium fistulosum</Emphasis>)

Summary The first genetic linkage map of Japanese bunching onion (Allium fistulosum) based primarily on AFLP markers was constructed using reciprocally backcrossed progenies. They were 120 plants each of (P₁)BC₁ and (P₂)BC₁ populations derived from a cross between single plants of two inbred lines: D1s-15s-22 (P₁) and J1s-14s-20 (P₂). Based on the (P₂)BC₁ population, a linkage map of P₁ was constructed. It comprises 164 markers – 149 amplified fragment length polymorphisms (AFLPs), 2 cleaved amplified polymorphic sequences (CAPSs), and 12 simple sequence repeats (SSRs) from Japanese bunching onion, and 1 SSR from bulb onion (A. cepa) – on 15 linkage groups covering 947 centiMorgans (cM). The linkage map of P₂ was constructed with the (P₁)BC₁ population and composed of 120 loci – 105 AFLPs, 1 CAPS, and 13 SSRs developed from Japanese bunching onion and 1 SSR from bulb onion – on 14 linkage groups covering 775 cM. Both maps were not saturated but were considered to cover the majority of the genome. Nine linkage groups in P₂ map were connected with their counterparts in P₁ map using co-dominant anchor markers, 13 SSRs and 1 CAPS.     

Integration of AFLP markers into a linkage map of sugar beet (Beta vulgaris L.)

The AFLP (amplified fragment length polymorphism) technique has been applied in establishing an extended linkage map of sugar beet. A total of 120 AFLPs were integrated into an existing linkage map based on RFLP markers. Four primer combinations yielded between 19 and 40 polymorphic bands in an F₂ population consisting of 94 plants. The AFLP loci were evenly distributed over the nine linkage groups, with the exception of linkage group V where the number of AFLPs was significantly low. The AFLPs were found to be reproducible even against the background of different combinations of Taq DNA polymerases and buffers. However, the quantity of higher molecular weight fragments (>400 bp) was reduced when using plant DNA of poor quality as a template. The results of these experiments are discussed, together with possible applications of AFLPs in sugar beet breeding.     

Construction of a genetic linkage map for witloof (Cichorium intybus L. var. foliosum Hegi)

A genetic linkage map based on an intraspecific cross between two inbred lines of witloof‐chicory (Cichorium intybus L. var. foliosum Hegi) has been constructed. In total, 129 RAPD markers were scored in 565 F₂ plants. Grouping of these markers at a LOD of threshold 4.0 resulted in nine linkage groups, which is equal to the chicory haploid genome. The nine linkage groups covered 609.6 cM. All 129 RAPD markers were linked to one of the nine groups. Three RAPD markers could not be mapped. Out of the 126 remaining RAPD markers, 18 showed segregation distortion with significance value of P < 0.01.     

QTL mapping of resistance in lentil (Lens culinaris ssp. culinaris) to ascochyta blight (Ascochyta lentis)

Quantitative trait locus (QTL) analysis of ascochyta blight resistance in lentil was conducted using genomic maps developed from two F₂ populations, viz. ILL5588/ILL7537 and ILL7537/ILL6002. Five QTLs for ascochyta blight resistance were identified by composite interval mapping (CIM) across four linkage groups (LG) in population ILL5588/ILL7537. Three QTLs were identified by CIM in population ILL7537/ILL6002 (two in close proximity on LGI and one on LGII). Two of these coincided with regions identified using multiple interval mapping (MIM) and were shown to be conditioned by dominant and partial dominant gene action. Together, they accounted for approximately 50% of the phenotypic variance of disease severity. Comparison between the two populations revealed a potentially common QTL and several common regions that contained markers significantly associated with resistance. This study demonstrated the transferability of QTLs among populations and identified markers closely linked to the major QTL that may be useful for future marker‐assisted selection for disease resistance.     

Development of EST-SSR markers and construction of a linkage map in faba bean (Vicia faba)

To develop a high density linkage map in faba bean, a total of 1,363 FBES (Faba bean expressed sequence tag [EST]-derived simple sequence repeat [SSR]) markers were designed based on 5,090 non-redundant ESTs developed in this study. A total of 109 plants of a ‘Nubaria 2’ × ‘Misr 3’ F₂ mapping population were used for map construction. Because the parents were not pure homozygous lines, the 109 F₂ plants were divided into three subpopulations according to the original F₁ plants. Linkage groups (LGs) generated in each subpopulation were integrated by commonly mapped markers. The integrated ‘Nubaria 2’ × ‘Misr 3’ map consisted of six LGs, representing a total length of 684.7 cM, with 552 loci. Of the mapped loci, 47% were generated from multi-loci diagnostic (MLD) markers. Alignment of homologous sequence pairs along each linkage group revealed obvious syntenic relationships between LGs in faba bean and the genomes of two model legumes, Lotus japonicus and Medicago truncatula. In a polymorphic analysis with ten Egyptian faba bean varieties, 78.9% (384/487) of the FBES markers showed polymorphisms. Along with the EST-SSR markers, the dense map developed in this study is expected to accelerate marker assisted breeding in faba bean.     

Construction of a high-density reference linkage map of tea (Camellia sinensis)

A few linkage maps of tea have been constructed using pseudo-testcross theory based on dominant marker systems. However, dominant markers are not suitable as landmark markers across a wide range of materials. Therefore, we developed co-dominant SSR markers from genomic DNA and ESTs and constructed a reference map using these co-dominant markers as landmarks. A population of 54 F₁ clones derived from reciprocal crosses between ‘Sayamakaori’ and ‘Kana-Ck17’ was used for the linkage analysis. Maps of both parents were constructed from the F₁ population that was taken for BC₁ population. The order of most of the dominant markers in the parental maps was consistent. We constructed a core map by merging the linkage data for markers that detected polymorphisms in both parents. The core map contains 15 linkage groups, which corresponds to the basic chromosome number of tea. The total length of the core map is 1218 cM. Here, we present the reference map as a central core map sandwiched between the parental maps for each linkage group; the combined maps contain 441 SSRs, 7 CAPS, 2 STS and 674 RAPDs. This newly constructed linkage map can be used as a basic reference linkage map of tea.     

利用大白菜抗感干烧心病F2群体构建AFLP遗传连锁图

大白菜(BrassicacampestrisL.ssp.pekinensis)原产于中国,是我国蔬菜栽培中分布最广、种植面积最大的蔬菜作物之一,也是我国的主要出口创汇蔬菜之一。但是近年来大白菜干烧心病却严重影响了其内部质量和出口创汇。此病是由于缺钙引起的生理性病害,不同品种间在抗干烧心病特性上表现出明显的差异,选育抗干烧心病品种值得引起关注。本实验利用大白菜离体叶片扦插方法,结合多年青岛农科院研究人员的田间观察对大量的大白菜品种进行广泛筛选,得到了抗病品种和感病品种。以大白菜抗干烧心病品种F1-6-5-2-2-2-3和感干烧心病品种P14-2-1-15杂交的F2代115个单株作为构建遗传图谱的群体,通过对192对引物组合的筛选,利用32对引物得到了280个AFLP多态性位点,经Jionmap3.0软件处理,得到了一张含105个标记位点、11个连锁群、覆盖长度为669.7cM的连锁图。每个连锁群上的标记数在4￣27之间,平均图距在3.3￣12.5cM之间,连锁群长度在23.4￣98.9cM之间。105个AFLP位点中偏离孟德尔遗传规律的比率为39.0%。为大白菜干烧心QTL定位和分析奠定了基础。     

Density enhancement of a faba bean genetic linkage map (Vicia faba) based on simple sequence repeats markers

Genetic mapping for faba bean lags far behind other major crops. Density enhancement of the faba bean genetic linkage map was carried out by screening 5,325 genomic SSR primers and 2033 expressed sequence tag (EST)‐SSR primers on the parental cultivars '91825' and 'K1563'. Two hundred and fifteen genomic SSR and 133 EST‐SSR primer pairs that detected polymorphisms in the parents were used to screen 129 F₂ individuals. This study added 337 more SSR markers and extended the previous linkage map by 2928.45 cM to a total of 4516.75 cM. The number of SSR markers in the linkage groups varied from 12 to 136 while the length of each linkage group ranged from 129.35 to 1180.21 cM. The average distance between adjacent loci in the enhanced genetic linkage map was 9.71 cM, which is 2.79 cM shorter than the first linkage map of faba bean. The density‐enhanced genetic map of faba bean will be useful for marker‐assisted selection and breeding in this important legume crop.     

Development of molecular linkage maps in sweet potato (Ipomoea batatas L.) using sequence‐related amplified polymorphism markers

Sweet potato is an important food crop with high starch content. It is a hexaploid species, for which the chromosomes have not yet been well characterized. In this study, we used 856 SRAP primer pairs to analyse the 240 individuals from a mapping population, which were derived from a hybrid F₁ generation of ‘Luoxushu 8’ (female) and ‘Zhengshu 20’ (male). Genetic linkage maps of the two parents were constructed. In the female parent (‘Luoxushu 8’), the linkage map consisted of 1391 markers, and the length of the linkage map was estimated to be 10,188.4 cM with an average distance of 7.17 cM between markers. In the male parent (‘Zhengshu 20’), the final linkage map consisted of 1,112 markers, and the estimated length of the map was 9,165.17 cM with an average distance of 8.40 cM between markers. Our results provide a basis for the detailed characterization of sweet potato chromosome sequences and the development of related molecular markers.     

Construction of high-density linkage map and identification of QTLs associated with resistance to black rot in radish (Raphanus sativus) by RAD sequencing

High-density marker-based QTL mapping can serve as an effective strategy to identify novel genomic information to facilitate crop improvement. In this study, we genotyped an F₂ population (KB12-1 × PP12-1) using a RAD-seq approach and constructed a high-density linkage map for radish. After a series of filtering procedures were performed, 17,124 SNPs and 3,336 indels with aa × bb genotyping were retained to obtain bin markers. Then, a linkage map comprising a total of 1,221 bin markers in nine linkage groups spanning 1,467.3 cM with an average marker interval of 1.2 cM was constructed. We evaluated the resistance of the F₂ mapping population to black rot using F₃ progeny, and two major QTLs related to black rot resistance were identified based on this map. Among these QTLs, qBRR2 on Chr.2 explained 26.97% of the phenotypic variation with a LOD score of 11.93, and qBRR7 on Chr.7 accounted for 27.06% of the phenotypic variation with a LOD score of 11.83. The additive effect of qBRR2 was positive (14.97); however, qBRR7 had the opposite effect (−11.99). The high-density linkage map and the major QTLs qBRR2 and qBRR7 provide new important information for disease resistance gene discovery and utilization in genetic improvement.