Genetic analysis of apomixis in Citrus and Poncirus by molecular markers

Propagation of citrus rootstocks depends upon the production of clonal plants from nucellar seedlings. This makes apomixis one of the host important traits in breeding programs for citrus rootstocks. The genetic control of apomixis was studied in a 50-tree progeny derived from the cross C. volkameriana×P. trifoliata using 69 molecular markers and bulked segregant analysis. The proportion of nucellar seedlings was estimated by isoenzymatic analysis of 25 seedlings per tree for 2 consecutive years. The type of embryony (polyembryonic versus monoembryonic seeds) was also determined for fruit-yielding trees. Separate genetic maps for each parental species were developed. The integration and comparison of these maps could be accomplished using common multiallelic segregant loci. Differences in gene synteny between the two species-specific genetic maps were shown. Important distortions in the segregation of markers at several genomic regions, some of them also involving differences in the C-methylation pattern, have been observed, especially for the pollen parent. Analysis of quantitative trait loci (QTLs) revealed the presence of six genomic positions (two in P. trifoliata and four in C. volkameriana) contributing individually up to 24% of the total variation for apomixis. Within the same species, QTLs with positive and negative allele effects were present, even in the same linkage group. One of the markers associated to apomixis (Apo2) is also associated to embryony type. Therefore, the genetic control of apomictic reproduction found in citrus (nucellar embryony) is quite complex compared to what has been reported for gametophytic apomixis. Molecular markers linked to QTLs governing apomixis will be useful to assist selection of future apomictic rootstocks for citrus varieties. Received: 30 November 1998 / Accepted: 28 December 1998     

AFLP markers closely linked to a major gene essential for nucellar embryony (apomixis<Emphasis Type="Italic">)</Emphasis> in <Emphasis Type="Italic">Citrus maxima</Emphasis> × <Emphasis Type="Italic">Poncirus trifoliata</Emphasis>

Some citrus varieties express a form of apomixis termed nucellar embryony in which the adventive embryos develop from nucellus tissue surrounding the embryo sac. This trait results in many seeds containing multiple embryos (polyembryony). Inheritance of the frequency of polyembryony was studied in 88 progeny from a cross of Citrus maxima (monoembryonic) × Poncirus trifoliata (polyembryonic). The frequency of polyembryonic seed produced by each progeny was determined by scoring 100–500 seeds for the number of seedlings to emerge from each seed. Two groups of eight individuals from each extreme of the population were chosen for bulked segregant analysis with amplified fragment length polymorphism markers amplified with 256 primer combinations. Candidate markers identified in the bulks as linked to the trait were tested on the 32 individuals used to create the bulks and then on the remaining plants in the population. Five candidate markers tightly linked to polyembryony in P. trifoliata were identified. Specific marker alleles were present in nearly all progeny that produced polyembryonic seed, and alternate alleles were present in nearly all progeny that produced only monoembryonic seed. The region defined by these markers very likely contains a gene that is essential for the production of polyembryonic seeds by apomixis, but also shows segregation distortion. The proportion of polyembryonic seeds varied widely among the hybrid progeny, probably due to other genes. Scoring 119 progeny of a P. trifoliata selfed population for the closely linked markers and the proportion of polyembryonic seeds confirmed close linkage between these markers and polyembryony.     

Comparative genome-wide segregation analysis and map construction using a reciprocal cross design to facilitate citrus germplasm utilization

Citrus genetic resources are rich but underutilized in breeding because their complex reproductive biology and the scarceness of inheritance studies on agronomic traits. Here, we investigated the genomic distribution of segregation distortion regions, the inheritance of organelle DNA and colinearity between scion citrus linkage maps by using a reciprocal cross design. The parents were Fortune, a hybrid mandarin from C. clementina, and Chandler, a hybrid pummelo from C. grandis that largely differ in fruit size, taste and colour. The inheritance of organelle DNA was studied in 201 hybrids by using four organelle DNA markers, and the linkage maps were based on 174 of those hybrids. Around ten percent of the seedlings derived from the pummelo as female parent showed the same organelle markers as those of the mandarin, indicating a possible exception to their expected maternal inheritance in citrus. Most segregation distortion affects just the allele frequencies, generally representing differences in pollen fertilization success, as a likely consequence of the presence of gametal factors affecting the functionality of gametes and pollen-pistil interactions. The large extension of colinearity found when comparing the C. grandis and C. clementina linkage maps to those previously reported for rootstock species (C. aurantium and P. trifoliata), will be helpful to infer the position of orthologous genes and QTLs in citrus species and for a more useful genetic characterization of citrus germplasm collections.     

Quantitative trait loci analysis of morphological traits in Citrus

The objectives of this study were to understand the genetic basis of morphological variation observed in the genus Citrus and its relatives and to identify genomic regions associated with certain morphological traits using genetic linkage mapping and quantitative trait loci (QTLs) analysis with random amplified polymorphic DNA (RAPD) markers. First, a genetic linkage map was constructed with RAPD markers obtained by screening 98 progeny plants from a {Citrus grandis × [C. paradisi × Poncirus trifoliata]} × {[(C. paradisi × P. trifoliata) × C. reticulata] × [(C. paradisi × Poncirus trifoliata) × C. sinensis]} intergeneric cross. The map contains 69 RAPD markers distributed into nine linkage groups. Then, 17 different morphological traits, including six tree and two leaf characters of 98 progeny plants and six floral and three fruit characters of about half of the same progeny plants were evaluated for 2 years and statistically analyzed for variation. Statistical analysis of individual traits indicated that trunk diameter and growth, tree height, canopy width, tree vigor and growth, leaf length and width, petal and anther numbers, petal length and width, length of pistil and style, fruit length and diameter, and fruit segment number showed normal or close to normal distribution, suggesting that these traits may be inherited quantitatively. Quantitative data from the morphological traits were analyzed to detect markers and putative QTLs associated with these traits using interval mapping method. QTL analysis revealed 18 putative QTLs of LOD > 3.0 associated with 13 of the morphological traits analyzed. The putative QTLs were distributed in several different linkage groups, and QTLs associated with similar traits were mostly mapped to the same LG or similar locations in the linkage group, indicating that the same genomic region is involved in the inheritance of some of the morphological traits.     

QTL mapping of mandarin (<Emphasis Type="Italic">Citrus reticulata</Emphasis>) fruit characters using high-throughput SNP markers

Seedlessness, flavor, and color are top priorities for mandarin (Citrus reticulata Blanco) cultivar improvement. Given long juvenility, large tree size, and high breeding cost, marker-assisted selection (MAS) may be an expeditious and economical approach to these challenges. The objectives of this study were to construct high-density mandarin genetic maps and to identify single nucleotide polymorphism (SNP) markers associated with fruit quality traits. Two parental genetic maps were constructed from an F₁ population derived from ‘Fortune’ × ‘Murcott’, two mandarin cultivars with distinct fruit characters, using a 1536-SNP Illumina GoldenGate assay. The map for ‘Fortune’ (FOR) consisted of 189 SNPs spanning 681.07 cM and for ‘Murcott’ (MUR) consisted of 106 SNPs spanning 395.25 cM. Alignment of the SNP sequences to the Clementine (Citrus clementina) genome showed highly conserved synteny between the genetic maps and the genome. A total of 48 fruit quality quantitative trait loci (QTLs) were identified, and ten of them stable over two or more samplings were considered as major QTLs. A cluster of QTLs for flavedo color space values L, a, b, and a/b and juice color space values a and a/b were detected in a single genomic region on linkage group 4. Two carotenoid biosynthetic pathway genes, pds1 and ccd4, were found within this QTL interval. Several SNPs were potentially useful in MAS for these fruit characteristics. QTLs were validated in 13 citrus selections, which may be useful in further validation and tentative MAS in mandarin fruit quality improvement.     

High-density linkage maps for <Emphasis Type="Italic">Citrus sunki</Emphasis> and <Emphasis Type="Italic">Poncirus trifoliata</Emphasis> using DArTseq markers

The construction of a high-resolution genetic map of citrus would be of great value to breeders and to associate genomic regions with characteristics of agronomic interest. Here, we describe a novel high-resolution map of citrus using a population derived from a controlled cross between Citrus sunki (female parent) and Poncirus trifoliata (male parent). The genetic linkage maps were constructed using DArTseq markers and a pseudo-testcross strategy; only markers showing the expected segregation ratio were considered. To investigate synteny, all markers from both linkage maps were aligned with the genome of Citrus sinensis. The C. sunki map has a total of 2778 molecular markers and a size of 2446.6 cM, distributed across ten linkage groups. The map of P. trifoliata was built with 3084 markers distributed in a total of nine linkage groups, with a total size of 2411.6 cM. These maps are the most saturated linkage maps available for C. sunki and P. trifoliata and have high genomic coverage. We also demonstrated that the maps reported here are closely related to the reference genome of C. sinensis.     

Quantitative trait locus (QTL) analysis of fruit-quality traits for mandarin breeding in Japan

The improvement of fruit quality is an important objective in citrus breeding. Using an F₁ segregating population from a cross between citrus cultivars ‘Harehime’ (‘E647’—‘Kiyomi’ [Citrus unshiu Marcow. ‘Miyagawa Wase’ × Citrus sinensis (L.) Osbeck ‘Trovita’] × ‘Osceola’—a cultivar of clementine [Citrus clementina hort. ex Tanaka] × ‘Orland’ [Citrus paradisi Macfad. ‘Duncan’ × Citrus tangerina hort. ex Tanaka] × ‘Miyagawa Wase’) and ‘Yoshida’ ponkan (Citrus reticulata Blanco ‘Yoshida’), a SNP-based genetic linkage map was constructed and quantitative trait locus (QTL) mapping of four fruit-quality traits (fruit weight, sugar content, peel puffing, and water rot) was performed. The constructed genetic linkage map of ‘Harehime’ consisted of 442 single nucleotide polymorphisms (SNPs) on 9 linkage groups (LGs) and covered 635.8 cM of the genome, while that of ‘Yoshida’ ponkan consisted of 332 SNPs on 9 LGs and covered 892.9 cM of its genome. We identified four QTLs associated with fruit weight, one QTL associated with sugar content, three QTLs associated with peel puffing, and one QTL associated with water rot. For these QTL regions, we estimated the haplotypes of the crossed parents and verified the founding cultivars that these QTLs were originated from and their inheritance in descendant cultivars using pedigree information. QTLs identified in this study provide useful information for marker-assisted breeding of citrus in Japan.     

Analysis of Segregation Distortion of Molecular Markers in F2 Population of Rice

A genetic linkage map comprising 148 SSR markers loci was constructed using an F₂ population consisting of 90 lines derived from a sub-specific cross between a japonica variety Nipponbare and an indica variety Guangluai-4. The F₂ population showed high significantly distorted segregations. Among these SSR markers, 49 markers (33.11%) showed the genetics distortion(P<0.05). Of them, 36 markers deviated toward male parent indica GuangLuAi-4 and 13 markers toward heterozygote, but none toward the female parent Nipponbare. It was found that the segregation distortion might be caused by gametophyte and zygote. Since most gametophyte loci and sterility loci were mapped in segregation distortion regions, it indicated that the segregation distortion may be caused by these gametophyte loci and sterility loci. Finally, this research also analyzed the skewed segregation of some markers, which had not been mapped on chromosome.     

QTL analysis of citrus tristeza virus-citradia interaction

Citrus tristeza virus (CTV) has caused the death of millions of trees grafted on sour orange (Citrus aurantium). However, this rootstock is very well adapted to the Mediterranean, semi-arid conditions. The aim of the present research is to genetically analyze the accumulation of CTV in a progeny derived from the cross between C. aurantium and Poncirus trifoliata, both resistant to CTV isolate T-346. Graft propagation of 104 hybrids was done on healthy sweet orange as a rootstock. Three months later, each rootstock was graft inoculated with two patches of infected tissue (isolate T-346). One, 2, and sometimes, 3 and 4 years after inoculation, hybrids and infected patches were tested for CTV by tissue-blot immuno-assay. Additionally, CTV multiplication was evaluated every year as the optical density of double-antibody sandwich enzyme-linked immuno-sorbent assay reactions. Linkage maps for P. trifoliata based on 63 markers, and for C. aurantium based on 157 markers, were used. Most molecular markers were microsatellites and IRAP (inter-retrotransposon amplified polymorphisms). Some analogues of resistance and expressed sequences were also included for candidate gene analysis.Resistance against CTV was analyzed as a quantitative trait (CTV accumulation) by QTL (quantitative trait loci) analysis to avoid the assumption of monogenic control. Three major resistance QTLs were detected where the P. trifoliata resistance gene, Ctv-R, had been previously located in other progenies. Up to five minor QTLs were detected (Ctv-A ₁ to Ctv-A ₅ ). A significant epistatic interaction involving Ctv-R ₁ and Ctv-A ₁ was also found. An analogue of a resistance gene is a candidate for Ctv-A ₃ , and two expressed sequences are candidates for Ctv-A ₁ and Ctv-A ₅ . Single-strand conformational polymorphism analysis of CTV genes QTL P20 and P25 (coat protein) in susceptible hybrids, was carried out to test whether or not any QTL accumulation was a defeated resistance gene. Since the same haplotype of the virus was visualized independently on the CTV titer, differences in the amount of virions are not explained through the selection of CTV genotypes by the host, but through differences among citradias in CTV replication and/or movement.Communicated by C. Möllers     

Chromosomal regions associated with segregation distortion in maize

Segregation distortion skews the genotypic frequencies from their Mendelian expectations. Our objectives in this study were to assess the frequency of occurrence of segregation distortion in maize, identify chromosomal regions consistently associated with segregation distortion, and examine the effects of gametophytic factors on linkage mapping. We constructed a simple sequence repeat (SSR) linkage map for a LH200/LH216 F₂Syn3 (i.e., random-mated three times) population, and compared the segregation distortion in this map with the segregation distortion in three published linkage maps. Among 1,820 codominant markers across the four mapping populations, 301 (17%) showed segregation distortion (P < 0.05). The frequency of markers showing segregation distortion ranged from 19% in the Tx303/CO159 mapping population to 36% in the B73/Mo17 mapping population. A positive relationship was found between the number of meioses and the frequency of segregation distortion detected in a population. On a given chromosome, nearly all of the markers showing segregation distortion favored the allele from the same parent. A total of 18 chromosomal regions on the ten maize chromosomes were associated with segregation distortion. The consistent location of these chromosomal regions in four populations suggested the presence of segregation distortion regions (SDRs). Three known gametophytic factors are possible genetic causes of these SDRs. As shown in previous research, segregation distortion does not affect the estimate of map distance when only one gametophytic factor is present in an SDR.     

Segregation and Linkage Analysis of 75 Novel Microsatellite DNA Markers in Pair Crosses of Japanese Abalone (Haliotis discus hannai) Using the 5′-Tailed Primer Method

We present novel microsatellite markers of the Japanese abalone (Haliotis discus hannai) for general mapping studies in this species. A total of 75 microsatellite markers were developed, and the allele-transmission patterns of these markers were studied in three families generated by pair crosses. For allele scoring, we employed the 5′-tailed primer polymerase chain reaction (PCR) technique, which substantially reduces the cost for fluorescent labeling of primers. Of the 225 possible marker-family combinations (75 markers × 3 families), 18 cases of informative null-allele segregation were inferred. When such null-allele segregations were allowed, more than 70% of the 75 markers in the families turned out to be markers with an expected segregation ratio of 1:1:1:1, allowing maximal exploitation of the codominant nature of microsatellite markers. There were 16 instances of segregation distortion at the 5% significance level. The test for independence of segregation assigned the 75 markers into 17 linkage groups, which is in close agreement with the haploid chromosome number of H. discus hannai (n = 18). Six markers could not be placed into any linkage group. We suggest that these markers could help construct a H. discus hannai linkage map.     

QTL analysis of cotton fiber length in advanced backcross populations derived from a cross between <Emphasis Type="Italic">Gossypium hirsutum</Emphasis> and <Emphasis Type="Italic">G. mustelinum</Emphasis>

Key message

QTLs for fiber length mapped in three generations of advanced backcross populations derived from crossing Gossypium hirsutum and Gossypium mustelinum showed opportunities to improve elite cottons by introgression from wild relatives.

Abstract

The molecular basis of cotton fiber length in crosses between Gossypium hirsutum and Gossypium mustelinum was dissected using 21 BC₃F₂ and 12 corresponding BC₃F_2:3 and BC₃F_2:4 families. Sixty-five quantitative trait loci (QTLs) were detected by one-way analysis of variance. The QTL numbers detected for upper-half mean length (UHM), fiber uniformity index (UI), and short fiber content (SFC) were 19, 20, and 26 respectively. Twenty-three of the 65 QTLs could be detected at least twice near adjacent markers in the same family or near the same markers across different families/generations, and 32 QTLs were detected in both one-way variance analyses and mixed model-based composite interval mapping. G. mustelinum alleles increased UHM and UI and decreased SFC for five, one, and one QTLs, respectively. In addition to the main-effect QTLs, 17 epistatic QTLs were detected which helped to elucidate the genetic basis of cotton fiber length. Significant among-family genotypic effects were detected at 18, 16, and 16 loci for UHM, UI, and SFC, respectively. Six, two, and two loci showed genotype?×?family interaction for UHM, UI and SFC, respectively, illustrating complexities that might be faced in introgression of exotic germplasm into cultivated cotton. Co-location of many QTLs for UHM, UI, and SFC accounted for correlations among these traits, and selection of these QTLs may improve the three traits simultaneously. The simple sequence repeat (SSR) markers associated with G. mustelinum QTLs will assist breeders in transferring and maintaining valuable traits from this exotic source during cultivar development.

     

QTL mapping for brown rot (Monilinia fructigena) resistance in an intraspecific peach (Prunus persica L. Batsch) F1 progeny

Brown rot (BR) caused by Monilinia spp. leads to significant post-harvest losses in stone fruit production, especially peach. Previous genetic analyses in peach progenies suggested that BR resistance segregates as a quantitative trait. In order to uncover genomic regions associated with this trait and identify molecular markers for assisted selection (MAS) in peach, an F1 progeny from the cross “Contender” (C, resistant)?×?“Elegant Lady” (EL, susceptible) was chosen for quantitative trait loci (QTL) analysis. Over two phenotyping seasons, skin (SK) and flesh (FL) artificial infections were performed on fruits using a Monilinia fructigena isolate. For each treatment, infection frequency (if) and average rot diameter (rd) were scored. Significant seasonal and intertrait correlations were found. Maturity date (MD) was significantly correlated with disease impact. Sixty-three simple sequence repeats (SSRs) plus 26 single-nucleotide polymorphism (SNP) markers were used to genotype the C?×?EL population and to construct a linkage map. C?×?EL map included the eight Prunus linkage groups (LG), spanning 572.92 cM, with an average interval distance of 6.9 cM, covering 78.73 % of the peach genome (V1.0). Multiple QTL mapping analysis including MD trait as covariate uncovered three genomic regions associated with BR resistance in the two phenotyping seasons: one containing QTLs for SK resistance traits near M1a (LG C?×?EL-2, R ²?=?13.1–31.5 %) and EPPISF032 (LG C?×?EL-4, R ²?=?11–14 %) and the others containing QTLs for FL resistance, near markers SNP_IGA_320761 and SNP_IGA_321601 (LG3, R ²?=?3.0–11.0 %). These results suggest that in the C?×?EL F1 progeny, skin resistance to fungal penetration and flesh resistance to rot spread are distinguishable mechanisms constituting BR resistance trait, associated with different genomic regions. Discovered QTLs and their associated markers could assist selection of new cultivars with enhanced resistance to Monilinia spp. in fruit.     

Extension of the linkage map in Citrus using random amplified polymorphic DNA (RAPD) markers and RFLP mapping of cold-acclimation-responsive loci

Genetic mapping with RAPD markers has been initiated in Citrus. Reproducible polymorphism of amplified DNA fragments was obtained with approximately half of the 140 random primers tested, revealing 266 segregating loci. These were tested for linkage using 60 BC₁ progeny from an intergeneric cross of Citrus grandis (L.) Osb. x [Citrus grandis (L.) Osb. x Poncirus trifoliata (L.) Raf.]. A core linkage map was constructed that consists of nine linkage groups containing 109 RAPD markers and 51 previously-mapped RFLP and isozyme markers. A further 79 markers that could not be ordered unambiguously because of their allelic constitution were associated with individual linkage groups and are shown in relation to the core map. The core map has a total length of 1192 cM with an average distance of 7.5 cM between loci and is estimated to cover 70–80% of the genome. Loci with distorted segregation patterns clustered on several linkage groups. Individual clusters of loci were skewed in allelic composition toward one or the other parent, usually C. grandis. This relatively-saturated linkage map will eventually be used to identify quantitative trait loci for cold and salt-tolerance in Citrus. As a beginning we have mapped three loci detected by a cold-acclimation-responsive cDNA.     

Quantitative trait loci for agronomic traits in an elite barley population for Mediterranean conditions

Advances in plant breeding through marker-assisted selection (MAS) are only possible when genes or quantitative trait loci (QTLs) can contribute to the improvement of elite germplasm. A population of recombinant inbred lines (RILs) was developed for one of the best crosses of the Spanish National Barley Breeding Program, between two six-row winter barley cultivars Orria and Plaisant. The objective of this study was to identify favourable QTLs for agronomic traits in this population, which may help to optimise breeding strategies for these and other elite materials for the Mediterranean region. A genetic linkage map was developed for 217 RILs, using 382 single nucleotide polymorphism markers, selected from the barley oligonucleotide pool assay BOPA1 and two genes. A subset of 112 RILs was evaluated for several agronomic traits over a period of 2 years at three locations, Lleida and Zaragoza (Spain) and Fiorenzuola d’Arda (Italy), for a total of five field trials. An important segregation distortion occurred during population development in the region surrounding the VrnH1 locus. A QTL for grain yield and length of growth cycle was also found at this locus, apparently linked to a differential response of the VrnH1 alleles to temperature. A total of 33 QTLs was detected, most of them for important breeding targets such as plant height and thousand-grain weight. QTL × environment interactions were prevalent for most of the QTLs detected, although most interactions were of a quantitative nature. Therefore, QTLs suitable for MAS for most traits were identified.     

QTLs for Tolerance of Drought and Breeding for Tolerance of Abiotic and Biotic Stress: An Integrated Approach

Background

The coupling of biotic and abiotic stresses leads to high yield losses in rainfed rice (Oryza sativa L.) growing areas. While several studies target these stresses independently, breeding strategies to combat multiple stresses seldom exist. This study reports an integrated strategy that combines QTL mapping and phenotypic selection to develop rice lines with high grain yield (GY) under drought stress and non-stress conditions, and tolerance of rice blast.

Methodology

A blast-tolerant BC₂F₃-derived population was developed from the cross of tropical japonica cultivar Moroberekan (blast- and drought-tolerant) and high-yielding indica variety Swarna (blast- and drought-susceptible) through phenotypic selection for blast tolerance at the BC₂F₂ generation. The population was studied for segregation distortion patterns and QTLs for GY under drought were identified along with study of epistatic interactions for the trait.

Results

Segregation distortion, in favour of Moroberekan, was observed at 50 of the 59 loci. Majority of these marker loci co-localized with known QTLs for blast tolerance or NBS-LRR disease resistance genes. Despite the presence of segregation distortion, high variation for DTF, PH and GY was observed and several QTLs were identified under drought stress and non-stress conditions for the three traits. Epistatic interactions were also detected for GY which explained a large proportion of phenotypic variance observed in the population.

Conclusions

This strategy allowed us to identify QTLs for GY along with rapid development of high-yielding purelines tolerant to blast and drought with considerably reduced efforts. Apart from this, it also allowed us to study the effects of the selection cycle for blast tolerance. The developed lines were screened at IRRI and in the target environment, and drought and blast tolerant lines with high yield were identified. With tolerance to two major stresses and high yield potential, these lines may provide yield stability in rainfed rice areas.     

A complete genetic linkage map and QTL analyses for bast fibre quality traits, yield and yield components in jute (Corchorus olitorius L.)

We report the first complete microsatellite genetic map of jute (Corchorus olitorius L.; 2n = 2 × = 14) using an F₆ recombinant inbred population. Of the 403 microsatellite markers screened, 82 were mapped on the seven linkage groups (LGs) that covered a total genetic distance of 799.9 cM, with an average marker interval of 10.7 cM. LG5 had the longest and LG7 the shortest genetic lengths, whereas LG1 had the maximum and LG7 the minimum number of markers. Segregation distortion of microsatellite loci was high (61%), with the majority of them (76%) skewed towards the female parent. Genomewide non-parametric single-marker analysis in combination with multiple quantitative trait loci (QTL)-models (MQM) mapping detected 26 definitive QTLs for bast fibre quality, yield and yield-related traits. These were unevenly distributed on six LGs, as co-localized clusters, at genomic sectors marked by 15 microsatellite loci. LG1 was the QTL-richest map sector, with the densest co-localized clusters of QTLs governing fibre yield, yield-related traits and tensile strength. Expectedly, favorable QTLs were derived from the desirable parents, except for nearly all of those for fibre fineness, which might be due to the creation of new gene combinations. Our results will be a good starting point for further genome analyses in jute.     

Exploiting BAC-end sequences for the mining,characterization and utility of new short sequences repeat (SSR) markers in Citrus

The aim of this study was to develop a large set of microsatellite markers based on publicly available BAC-end sequences (BESs), and to evaluate their transferability, discriminating capacity of genotypes and mapping ability in Citrus. A set of 1,281 simple sequence repeat (SSR) markers were developed from the 46,339 Citrus clementina BAC-end sequences (BES), of them 20.67% contained SSR longer than 20 bp, corresponding to roughly one perfect SSR per 2.04 kb. The most abundant motifs were di-nucleotide (16.82%) repeats. Among all repeat motifs (TA/AT)n is the most abundant (8.38%), followed by (AG/CT)n (4.51%). Most of the BES-SSR are located in the non-coding region, but 1.3% of BES-SSRs were found to be associated with transposable element (TE). A total of 400 novel SSR primer pairs were synthesized and their transferability and polymorphism tested on a set of 16 Citrus and Citrus relative’s species. Among these 333 (83.25%) were successfully amplified and 260 (65.00%) showed cross-species transferability with Poncirus trifoliata and Fortunella sp. These cross-species transferable markers could be useful for cultivar identification, for genomic study of Citrus, Poncirus and Fortunella sp. Utility of the developed SSR marker was demonstrated by identifying a set of 118 markers each for construction of linkage map of Citrus reticulata and Poncirus trifoliata. Genetic diversity and phylogenetic relationship among 40 Citrus and its related species were conducted with the aid of 25 randomly selected SSR primer pairs and results revealed that citrus genomic SSRs are superior to genic SSR for genetic diversity and germplasm characterization of Citrus spp.     

QTL analysis of yield and seed number in Citrus

Amount, regularity and low seed content of the crop are important properties of scion citrus cultivars. The genetic control of these traits was studied in a progeny derived from the cross Citrus volkameriana×Poncirus trifoliata using molecular marker analysis. Since the traits were not normally distributed, the Kruskal-Wallis non-parametric test was used for quantitative trait loci (QTLs) detection. Most of the QTLs detected correspond to the trait ”number of fruits per tree”, in agreement with its known physiological complexity. Related traits (fruit number, fruit size and seed number) are controlled by QTLs some of which are located in the same genomic regions, suggesting that undesired associations could be broken to some degree by recombination. QTL analysis over years revealed important effects of genotype-by-environment interaction on QTL detection. This result agrees with the differences found for the trait means among years, which was found to be related, among other causes, to the alternate bearing of some genotypes and the amount of rain before harvest. Received: 1 October 1999 / Accepted: 2 December 1999