Breeding banana (Musa spp.) for drought tolerance: A review

Drought is a major abiotic stress affecting banana production worldwide, leading to yield losses of up to 65%. Consequently, numerous efforts to understand and mitigate drought effects that include developing tolerant crop varieties are ongoing in several banana breeding programmes. The breeding efforts, however, have been greatly slowed down by inherent banana problems (polyploidy and male or female sterility) and complexity of drought tolerance (reportedly controlled by several genes). This review summarizes the pertinent research findings on water requirements of banana for its proper growth and productivity, symptoms of drought-sensitive varieties and field management strategies to cope with drought stress. The coping strategies deployed by resistant cultivars include high assimilation rates and water retention capacity as well as minor losses in leaf area and gaseous exchange. Reduced bunch weight, leaf chlorosis, wilting and strangled birth are underlined to be directly associated with drought susceptibility. Integration of conventional, molecular breeding and biotechnological tools as well as exploitation of the existing banana genetic diversity presents a huge opportunity for successful banana improvement.     

A review on adaptation of banana (Musa spp.) to cold in subtropics

Global production of bananais adversely affected by abiotic stresses, namely, drought, salinity and low temperature which cause changes in morphology, anatomy, physiology and biochemical metabolism in plant. Different banana cultivars respond differently when grown in subtropical regions due to changes in temperature mainly at the time of flowering and fruiting. The subtropical regions persist cold in winter which become a major constraint for proper growth and development of banana. Only few cultivars are identified for cold tolerance. The cold tolerance is a complex phenomenon, involving numbers of interrelated metabolic pathways. With the onset of cold, growth decrease through alteration in the synthesis of metabolites which are regulated by expression of genes and their interactions. Recently, complete genome sequencing, mutation and transgenesis provided deep insight into the complex mechanism of cold tolerance in banana. In this review, efforts are made to compile the findings and to interpret the better application of technologies in understanding the cold tolerance which may assist in banana breeding.     

Rheological and chemical predictors of texture and taste in dessert banana (Musa spp.)

To be able to account for sensory qualities earlier in the assessment of a new banana hybrid in a selection scheme, predicting the sensory perception of banana texture and taste by instrumental parameters was investigated. Thirteen cultivated banana and four new triploid hybrids were characterized by sensory profiling, and rheological and chemical analyses. Multilinear regressions were used to calibrate predictions using 13 cultivated bananas, and the quality of predictions was validated using four hybrids. The sensory characteristics sourness and sweetness were predicted by titratable acidity (R² = 0.68) and pH (R² = 0.66). Malate and citrate were the main contributors to sweetness and sourness. Astringency was predicted by total tannins (R² = 0.55). Rheological parameters from texture profile analyses (stress at fracture, fracturability) were more suitable than pulp puncture force to predict the sensory texture properties firmness (R² = 0.47) and melting (R² = 0.60). These textural properties were predicted by titratable acidity and dry matter content (R² = 0.62). Predictions of mealiness, adhesiveness, and heterogeneity were not efficient. Differences of 3.6–3.7 meq 100 g⁻¹ FW in titratable acidity or of 0.30 g 100 g⁻¹ FW in malate or citrate were required to ensure a detectable difference in sourness or sweetness (p = 0.9). Pulp puncture force needed to differ by a minimum of 0.9 N before a difference in firmness could be perceived by the panelists. In conclusion, while models to predict sourness and sweetness can now be used for high throughput phenotyping, we recommend additional tests for other sensory attributes.     

Genome classification of banana cultivars from South India using IRAP markers

Summary The banana cultivars are originated from the intra- and inter-specific hybridization of two wild diploid species, Musa acuminata Colla and Musa balbisiana Colla, contributing the A and B genomes, respectively. They are classified into genomic groups by scoring morphological features. Molecular markers provide a quick and reliable system of genome characterization and manipulation in breeding lines. In the present study a PCR based molecular marker specific for B genomes is been reported. The IRAP primer, designed based on the LTR sequence of banana Ty3-gypsy-like retroelement (Musa acuminata Monkey retrotransposon, AF 143332), was used to identify the B genome in the banana cultivars. Further a primer pair designed from B specific bands of Musa balbisiana `Pisang Gala' was used to classify AAB and ABB cultivars in the collection. Among the 36 cultivars tested with this primer, the B specific band was absent in the AA and AAA cultivars (except in one AAA and AAB cultivar) but present in all other AB, AAB and ABB cultivars. Among the triploid AAB/ABB, the PCR products with B specific primers showed restriction pattern polymorphism with AluI. In ABB genomes the band intensity was high whereas low intensity band observed in AAB genomes. Four cultivars reported to have the ABB genome showed a pattern similar to AAB, and one cultivar reported to have AAA genome showed a pattern similar to ABB genome, suggesting missampling or misidentification. The primers used in this study are useful to identify the presence of B genome in banana cultivars, and band intensity may be a preliminary indicator of ploidy level of the B genome but needs further studies with competitive PCR for clarification. These authors contributed equally in this paper.     

Isozyme electrophoretic characterization of 29 related cultivars of lily (Lilium spp.)

Isozyme banding patterns (IBPs) were studied for cultivars of lily (Lilium spp.) by means of horizontal starch‐gel electrophoresis (SGE). An array of continuous histidine‐citrate buffer systems at eight ranges of pH and four extraction buffers were tested. On the basis of this survey, the extraction buffer two (Eb‐2) and the buffer system E at pH 7.7 were found to be suitable for detection of lily isozymes. Using the SGE technique, IBP in catalase (CAT; EC 1.11.1.6), esterase (EST; EC 3.1.1.1), malate dehydrogenase (MDH; EC 1.1.1.37), malic enzyme (MAL; EC 1.1.1.40), peroxidase (POX; EC 1.11.1.7), phosphoglucomutase (PGM; EC 2.7.5.1), phosphoglucose isomerase (PGI; EC 5.3.1.9) and 6‐phosphogluconate dehydrogenase (PGD; EC 1.1.1.44) were assayed. In total 29 cultivars were tested in this study: nine were analysed for all eight enzyme systems, 16 cultivars for seven systems, three for six, and one for five enzyme systems. Some IBP were identified as section‐specific biochemical markers. Eight enzymes systems were analysed by constructing a dendogram using the unweighted pair group method, arithmetic average (UPGMA) cluster analysis. The analysis indicated that the lily cultivars could be separated from other Lilium species, except for two L. x formonlogi cultivars:‘Hakuba’ and ‘Hakuko’ which could not be distinguished from each other by the isozyme patterns assayed here. This study shows that isozymes can provide useful biochemical markers for lily cultivar identification and to estimate the phylogenetic relationships among those cultivars.     

Screening for scab resistance by RAPD markers in cultivars of apple (Malus spp.)

Genetic markers are a much faster and more practical alternative to classical methods for the identification of genes for scab resistance present in different apple cultivars. In our study, 28 scab-resistant cultivars, four wild sources of the resistance genes and 10 susceptible cultivars were screened for the presence of the RAPD fragments OPM18/900, OPD20/600 and OPA15/900, which are reported to be linked to the Vf gene. All three marker fragments were successfully amplified with different protocols in Vf-resistant cultivars including ‘M. floribunda 821’. No marker fragments were amplified in susceptible cultivars, three out of four Va-resistant cultivars, three out of four Vm-resistant cultivars, two Vr-resistant cultivars, ‘Antonovka PI 172612’ and ‘M. pumila R 12740-7A’. All three markers were found in the cv. ‘Nova Easygro’, reported to possess the Vr gene, and the cv. ‘Reglindis’, reported to be Va-resistant. M. atrosanguinea of unknown origin showed the presence of OPD20/600 and OPA 15/900 marker bands. The cvs. ‘Nova Easygro’, ‘Reglindis’ and M. atrosanguinea are probably carriers of the VF gene.     

Genetic diversity among pearl millet maintainers using microsatellite markers

Genetic diversity among 70 maintainers and two pollinators of sub-Saharan and Indian origin was studied for simple sequence repeat (SSR) loci using 34 primer pairs. A total of 213 alleles were detected with an average of 6.26 alleles per locus. Polymorphic information content (PIC) ranged from 0.05 to 0.96 with a mean of 0.58 for the SSR loci. Mean PIC across the linkage groups and number of alleles in dinucleotide motifs varied significantly. The lowest PIC (0.239) for linkage group 6 indicated comparatively conserved nature of this linkage group. Genetic similarity estimates ranged from 0.05 to 0.73 with an average value of 0.29. This indicated sufficient diversity among the maintainer and pollinator lines. The 72 lines fell in five clusters, and the clustering pattern corroborated with their pedigree and characteristic traits. Pollinator ICMR 356 was more diverse from the maintainer lines analysed, and can be a potential parent for pearl millet hybrid development.     

Genic microsatellite markers for discrimination of spinach cultivars

A set of simple sequence repeat (SSR or microsatellite) markers was used to discriminate a collection of 33 Spinacia oleracea hybrid cultivars from seven different breeding stations all over the world. All SSR markers were genic microsatellite markers located in coding or non-coding regions of genes of known function. Cluster analysis based on 13 of the SSR markers showed that the spinach hybrids grouped into three clusters. The first two clusters consisted of European spinach types, which were well discriminated according to their origin from different breeding stations. The third cluster was a mixture of Asian as well as European types of spinach. Subclusters in this group did not reflect differences in morphology, earliness or company origin. The data show that genic microsatellites are a powerful tool for discrimination of spinach cultivars.     

Development,characterization and mapping of microsatellite markers for lentil (Lens culinaris Medik.)

Lentil is the sixth most important pulse crop terms of production in the world, but the number of available and mapped SSR markers are limited. To develop SSR markers in lentil, four genomic libraries for (CA)n, (GA)n, (AAC)n and (ATG)n repeats were constructed. A total of 360 SSR primers were designed and validated using 15 Turkish lentil cultivars and genotypes. The most polymorphic repeat motifs were GA and CT, with a mean number of alleles per locus of 7.80 and 6.55, respectively. Seventy‐eight SSR primers amplified a total of 400 polymorphic alleles, whereas 71 SSR primers produced markers within the expected size range. For 78 polymorphic SSR primers, the average number of alleles per locus was 5.1 and PIC value ranged from 0.07 to 0.89, with an average of 0.58. A linkage map was constructed using 92 individual F₂ plants derived from a cross between Karacada? × Silvan, with 47 SSR markers. The SSR markers developed in this study could be used for germplasm classification and identification and mapping of QTL in lentil.     

利用微卫星和线粒体DNA标记研究山羊群体间的遗传关系

本研究利用微卫星和线粒体DNA分析山羊的遗传多样性及系统进化关系,用25个微卫星位点分析了安哥拉山羊、山东莱芜黑山羊、罕山白绒山羊、太行山羊及乌珠穆沁绒山羊这5个山羊品种的遗传多样性,共祖遗传距离的UPGMA聚类表明遗传距离和地理距离是一致的,如内蒙的罕山白绒山羊和乌珠穆沁绒山羊聚到一起。利用线粒体DNA分析安哥拉山羊、山东莱芜黑山羊、鲁北白山羊、太行山羊及乌珠穆沁绒山羊,揭示这5个山羊品种分成A和C 2个支系,并进行了群体结构和群体扩张分析。通过比较2种分子标记的分析结果,发现利用微卫星来研究群体的遗传多样性及品种间的关系具有较高的准确性,而线粒体在研究群体系统进化具有一定的优势,在分析品种间关系方面可能不是理想标记。     

Analysis of the genetic diversity among mandarins (Citrus spp.) using RAPD markers

RAPD markers were used to evaluate genetic similarity among 35 mandarin accessions, including 10 species and 7 hybrids. One octamer and twenty-two decamer primers produced 109 RAPDs, 45 of which were polymorphic. Jaccard coefficient was used to calculate genetic similarity, and UPGMA to generate the phenogram. The RAPDs obtained were sufficient to generate some accession-specific markers, and to separate these accessions by clustering them into several groups, many of them according to Tanaka's or Webber's systematic units. The genetic similarity within the mandarin group is high (G_J = 0.77), and suggests that cultivated mandarins have a narrow genetic base. The genetic similarity of mandarins to other true citrus species (Citron [C. medica L.] and Pummelo [C. grandis Osbeck]) was much lower (minimum G_J = 0.27). We propose that the mandarin group is a single species, C. reticulata Blanco, composed of several genetically different individuals and a great number of hybrids, rather than a large number of species as proposed by some taxonomic studies. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic relationships of avocado (Persea americana Mill.) using RAPD markers

RAPD (randomly amplified polymorphic DNA) analysis was carried out on 16 accessions representing the three ecological races of avocado (Persea americana Mill.), and one accession of P. schiedeana Nees. Twenty two preselected primers produced 133 polymorphic DNA fragments in the RAPD assay of the avocado accessions. One primer was identified which could differentiate each of the avocado accessions. Potentially race-specific markers for each of the Mexican, Guatemalan, and West Indian races, have been detected. A Jaccard's similarity coefficient matrix was generated and a dendrogram constructed using UPGMA (unweighted pair-group method of arithmetic averages) cluster analysis. Percentage similarity between avocado accessions ranged from 46% to 85%. The lowest similarity (between 22% and 29%) was revealed between P. schiedeana and any P. americana accession. Average similarity within races of avocado was 75% for the Mexican race, 71% for the West Indian race and 73% for the Guatemalan race. Average similarity between races ranged from 53% to 58%. The dendrogram identified three groups, representing the races of avocado. These results are in concordance with the present classification of avocado into three subspecies (varieties) of P. americana, namely drymifolia, americana, and guatemalensis, corresponding to the Mexican, West Indian and Guatemalan races, respectively, and confirm the separate species status of P. schiedeana. We conclude that RAPD markers may be useful for the classification of avocado and for the assessment of genetic diversity of avocado germplasm. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic diversity,structure and fruit trait associations in Greek sweet cherry cultivars using microsatellite based (SSR/ISSR) and morpho-physiological markers

It is important to couple phenotypic analysis with genetic diversity for germplasm conservation in gene bank collections. The use of molecular markers supports the study of genetic marker-trait associations of biological and agronomic interest on diverse genetic material. In this report, 19 Greek traditional sweet cherry cultivars and two international cultivars, which were used as controls, were grown in Greece and characterized for 17 morpho-physiological traits, 15 simple sequence repeat (SSR) loci and 10 inter simple sequence repeat (ISSR) markers. To our knowledge, this is the first report on molecular genetic diversity studies in sweet cherry in Greece. Principal component analysis (PCA) of nine qualitative and eight quantitative morphological parameters explain over 77.33% of total variability in the first five axes. The SSR markers yielded a combined matching probability ratio (MPR) of 9.569 × e−12. The 15 SSR loci produced a total of 92 alleles. Ten ISSR primers generated 91 bands, with an average of 9.1 bands per primer. Expected heterozygosity (gene diversity) values of 15 SSR loci and 10 ISSR markers averaged at 0.683 and 0.369, respectively. Based on stepwise multiple regression analysis (MRA), SSR alleles were found associated with harvest time and fruit polar diameter. Furthermore, three ISSR markers were correlated with fruit harvest and soluble solids and four ISSR markers were correlated with fruit skin color. Stepwise MRA identified six SSR alleles associated with harvest time with a high correlation (P < 0.001), with linear associations with high F values. Hence, data analyzed by the use of MRA could be useful in marker-assisted breeding programs when no other genetic information is available.     

Genetic variation among cultivars of red clover (Trifolium pratense L.) detected by RAPD markers amplified from bulk genomic DNA

Summary The use of random amplified polymorphic DNA (RAPD) markers obtained from bulked samples was investigated for cultivar identification in red clover. Pooled samples were examined in order to minimize variation within cultivars. To determine the appropriate number of individuals to include in the bulked samples representing each cultivar, DNA samples from two, three, four, five, ten and twenty individuals were pooled. Twenty was found to be an appropriate number of red clover individuals per bulk in order to amplify only the DNA sequences shared among most individuals in each cultivar. Fourteen 10-mer primers were used to amplify genomic DNA from combined leaf samples of 15 red clover cultivars from European, Japanese and North American origins. A total of 79 amplified products, of which 55 were polymorphic, was obtained. Cultivar-specific bands were observed with 13 primers. The amplification patterns obtained from two primers could distinguish all 15 red clover cultivars. Rogers' genetic distances for all 105 pairwise comparisons were calculated to evaluate relationships among these cultivars. Cluster analysis based on these genetic distances separated these 15 cultivars into three groups, with two of the groups consisting of a single Japanese cultivar each, while the third group included cultivars from European, North American, and Japanese origins.     

Genetic diversity of wild coffee (Coffea arabica L.) using molecular markers

Genetic diversity was studied using RAPD markers among119 coffee (Coffea arabica L.) individuals representing 88 accessions derived from spontaneous and subspontaneous trees in Ethiopia, the primary centre of species diversity, six cultivars grown locally in Ethiopia, and two accessions derived from the genetic populations Typica and Bourbon, spread in the 18^th century, which gave rise to the most currently grown cultivars. Twenty-nine polymorphic fragments were used to calculate a similarity index and construct dendrograms. The Ethiopian material was separated from the Typica- and Bourbon-derived accessions and classified in four groups: one with most of the collected material from southwestern Ethiopia and three from southern and southeastern Ethiopia. Almost all detected diversity was found in the southwestern group while the southern and southeastern groups presented only 59% of identified markers. The genetic distances were low between the southwestern group and the southern and southeastern groups, and between the southwestern group and the Typica- and Bourbon-derived accessions. The cultivated coffee derived from the genetic populations Typica and Bourbon appeared little differentiated from wild coffee growing in the southwest. The results supported the hypothesis that southwestern Ethiopian coffee trees could have been introduced recently in the south and southeast. A separate analysis of the 80accessions classified in the southwestern group allowed identifying particular spontaneous- and subspontaneous-derived accessions and redundancies in the collected material from southwestern Ethiopia. RAPD markers did not detect any within-collection polymorphism except for two trees that were identified as off-types in the CATIE field genebank. This revised version was published online in July 2006 with corrections to the Cover Date.     

Assessment of the uniformity and stability of grapevine cultivars using a set of microsatellite markers

Solidity of microsatellite markers is a key issue for varietal identification, especially when they are used for legal purposes, what includes their probable future use in the distinctness, uniformity and stability testing of new varieties needed for the granting of Plant Breeders’ Rights. Nine grapevine microsatellites (VVS2, VVMD5, VVMD27, VVMD28, ssrVrZAG29, ssrVrZAG62, ssrVrZAG67, ssrVrZAG83 and ssrVrZAG112), which had previously demonstrated its capacity to discriminate any grapevine variety, have been assessed to evaluate its uniformity and stability. 19 varieties were selected, representative of a high diversity for morphological, agronomical, cultural and historical aspects, as well as for microsatellite allele variability. Then, for each variety, uniformity and stability were evaluated through the analysis of 50 plants from each of three different plots, and five plants from each of seven additional plots. Material from 4,137 plants of 229 plots of the 19 varieties was sampled in seven countries. Of 3,654 plants analyzed with the set of nine microsatellites, 3,299 were of the right variety and used for the survey. An average of 172 individual values was studied for each allele of each microsatellite of each variety, and none differences were detected that could not be explained as technical variations, with the exception of several putative chimeras in two varieties. Of the total of 171 variety x microsatellite combinations, only in one combination (‘Merlot’ x VVMD27) the number of off-types exceeded the threshold allowed. The remaining 170 combinations have been found uniform and stable according to internationally accepted rules.