Allochrony as a potential driver for reproductive isolation in adaptive radiations of European whitefish ecomorphs

In northern Fennoscandian lakes, monophylogenetic lineages of postglacial fishes are radiating into several adaptive forms, but the speciation process is still at an incipient stage. The speciation process has received increased attention over the years, but the underlying mechanisms and drivers are still debated and poorly understood. European whitefish (Coregonus lavaretus [L.]) is the most abundant fish species in these lakes and has evolved into several ecomorphs adapted to different trophic niches and habitats. Genetic divergence has been observed among these ecomorphs, but the mechanism(s) responsible for the ongoing build-up of reproductive isolation has still to be revealed. As these systems are young in evolutionary time (<10 kyr), prezygotic and postzygotic extrinsic isolation mechanisms are thought to be more likely to contribute to the reproductive isolation than intrinsic isolation mechanisms. We determined the gonadosomatic index (GSI) of three ecomorphs in two replicated lake systems and used GSI as a proxy to investigate the prezygotic isolation mechanism, allochrony, as a driving factor of divergence in this adaptive radiation of whitefish. We found that the three ecomorphs differed in GSI values within and between lakes, suggesting different spawning times of the ecomorphs. We also show that males of one ecomorph had equal onset of maturity as another ecomorph, giving novel insights into the ongoing gene flow observed between ecomorphs. The result supports allochrony as a driver for the divergence process of whitefish ecomorphs, but more evidence is still needed to rule out that the three ecomorphs make use of different spawning grounds.     

Log Characteristics and Sawn Timber Recovery of Home-Garden Teak from Wet and Dry Localities of Kerala, India

There is a widely held view among smallholders that teak timber produced from small-scale agroforestry systems, especially home-garden forestry, fetches a lower price than that from conventional plantation forestry. To examine the veracity of this view, the wood quality attributes of teak from two home gardens in the district of Ernakulam (wet site) and Palakkad (dry site) in India were compared to those of forest plantation in Nilambur. The logs were graded using standard timber trade practices into high, medium and low quality as determined by the potential sawn timber grade-yield recovery pattern. Of 96 home garden teak logs (aged 35 years) from wet and dry sites, 59% belonged to timber Grade II–IV and the rest were classified as poles. Grade I logs (export quality) with a girth above 150 cm were not available from either of the homesteads. Faster-grown teak in the wet site produced large diameter logs (dbh 1.37 m) with average diameter of 39.6 cm, which is comparable to that of best site quality in India. In contrast, the average dbh for teak grown in the dry site was 24 cm as compared to the average dbh of 31 cm recorded from the same aged forest plantation in Nilambur. It was found that only 10% of logs belonged to Grade II timber and the rest fell under grades III and IV with more frequent visual defects. The sawn timber recovery percentage was lower for the dry site (66.8%), whereas there was no significant difference in grade from the wet and forest plantation sites, with recovery rates of 76.5% and 78.8%, respectively. The general notion that home garden teak has a large proportion of sapwood seems to be baseless, no significant difference being found between the heartwood-sapwood ratio of home-garden and forest plantation teak. Lack of appropriate silvicultural practices in home-garden forestry caused the production of more defective logs, adversely affecting the market price of timber.

Identification of a diverse mini‐core panel of Indian rice germplasm based on genotyping using microsatellite markers

Identification of a small core germplasm set representing the available genetic diversity is essential for its proper evaluation and subsequent utilization in rice improvement programmes. For constituting a small diverse mini‐core panel of Indian rice germplasm, a representative set of 6912 accessions drawn based on their geographic origin from the whole rice germplasm collection available in the National Gene Bank was genotyped using 36 microsatellite markers. Automated fragment analysis of amplicons yielded a total of 435 alleles, with an average 12.4 and range of 3–29 alleles per locus. Polymorphism information content (PIC) ranged from 0.08 (RGNMS190) to 0.86 (RM552) with an average of 0.528. Based on genotyping data, a mini‐core consisting of 98 genotypes was identified. Ninety‐four per cent of the alleles present in the core set were present in the mini‐core. The identified small but diverse panel will be useful for further intensive trait‐specific evaluation and utilization in allele mining.     

A unique introgression from Moricandia arvensis confers male fertility upon two different cytoplasmic male-sterile lines of Brassica juncea

A Brassica juncea line carrying an introgression from Moricandia arvensis restored male fertility to two cytoplasmic male‐sterile (CMS) B. juncea lines carrying either M. arvensis or Diplotaxis catholica cytoplasm. Genetics of fertility restoration was studied in the F₁, F₂, F₃ and backcross generations of the cross between CMS and fertility‐restorer lines. No male‐sterile plants were found in F1‐F₃ generations of the cross between CMS [M. arvensis] B. juncea and the restorer. However, a 1: 1 segregation for male sterility and fertility was observed when the F1 was pollinated with non‐restorer pollen from a euplasmic line. These results clearly show that restoration is mono‐genic and gametophytic. In CMS lines carrying D. catholica cytoplasm, the restorer conferred male fertility to the F1 and showed 3: 1 and 1: 1 segregations for male fertility and sterility in F₂ and BC1 generations, respectively, indicating a monogenic, sporophytic mode of fertility restoration. The results were also supported by pollen stainability in the F1 which was about 65% in M. arvensis‐based CMS and >90% in D. catholica‐based CMS. The above results are discussed in the light of previous molecular studies which showed association between CMS and atpA in both systems.     

Recent advances in molecular marker techniques: Insight into QTL mapping,GWAS and genomic selection in plants

Recent advances in sequencing technology have brought several novel platforms for marker development and subsequent genotyping. The high-throughput and cost effective marker techniques have changed the entire scenario of marker applications. The huge genotypic data obtained with next generation sequencing (NGS) also demands analytical tools, statistical advances, and comprehensive understanding to cope with breeding applications. In the present review, we discussed different available marker techniques, their strengths, and limitations. Emphasis was given on software tools, analytical pipelines, workbenches, and online resources available for marker development. Comparison of SNP genotyping involving complexity reduction techniques like GBS, RRL, RAD, and array-based platforms were presented in a view to describe suitability for specific purposes. We found that genotyping by whole genome re-sequencing has great potential, and could be a routine application in the near future with continuously decreasing cost of sequencing. Microsatellites, still a valuable option for breeders, have also advanced with NGS. Here a catalogue of tools for microsatellite evaluation in short sequence reads was provided. The most common applications of molecular marker like QTL mapping, genome-wide association mapping (GWAS), and genomic selection were highlighted. The present review will be helpful for the effective utilization of available resources and for the planning of crop improvement programs employing molecular marker techniques.     

Reaction of Lycopersicon cultivars and wild accessions to tomato leaf curl virus

Summary 1201 tomato cultivars, breeding lines and accessions of Lycopersicon species were screened for tomato leaf curl virus (TLCV) under field and laboratory conditions during summer seasons of 1986 to 1989. Two lines of L. hirsutum (PI 390658 and PI 390659) and 2 lines of L. peruvianum (PI 127830 and PI 127831) were resistant to TLCV infection. These accessions did not produce any leaf curl symptoms either in field or after inoculation by whitefly Bemisia tabaci with TLCV. Adult whiteflies died within 3 days after releasing on resistant accessions (PI 390658, PI 390659, PI 127830), whereas the whiteflies survived upto 25 days on susceptible tomato cultivars. Under field conditions 0–4 and 5–25 adult whiteflies were observed on resistant and susceptible cultivars respectively. Hybridization was effected using the popular tomato cultivars Arka Sourabh, and Arka Vikas, as the female parents and the resistant Lycopersicon wild species as the pollen parents, to incorporate the resistant gene(s) into the edible tomatoes.     

Population improvement in pyrethrum (Chrysanthemum cinerariaefolium Vis.)

Summary A population improvement programme in pyrethrum had progressively increased the mean pyrethrins content from 1.33 percent in the unselected base population to 1.97 percent in the population developed after one cycle of each of mass and recurrent selections. The selection had also increased the range of variation and the relative frequency of desirable plants.     

RFLP characterization of Indian Musa germplasm for clonal identification and classification

Summary Nineteen single-copy clones isolated from a PstI genomic library (cv. Maiden Plantain), and eight Vigna chloroplast DNA clones were used to probe total genomic DNA digests of 57 genotypes of Musa from India. The 19 genomic clones detected a total of 107 polymorphisms among the 57 genotypes. Principal coordinates and phenetic analyses of these data placed cultivars and species into distinct groups that were in general agreement with a previously published RAPD-based classification of these same plant materials. The 107 polymorphisms were sufficient to differentiate each clone from every other clone. Heterologous Vigna chloroplast DNA probes were used to characterize the cytoplasm of Musa cultivars and species. PCO analysis of these RFLPs were detected both within and between the generally recognized genome groups, indicating multiple hybridization pathways in the origin of hybrid clones. Data presented demonstrate that RFLPs are sufficiently abundant to classify Musa germplasm and that genetic relationships among Musa cultivars, based upon RFLP data, are in general agreement with relationships determined by analysis of morphology and RAPDs.     

The implications of 2n egg gametes in nobilization and breeding of sugarcane

Summary Nobilization in sugarcane is viewed from a genetic angle considering the significance of 2n gametes. The inbreeding coefficients resulting from 2n gametes, for first and second nobilizations are worked out. The implication of 2n gametes to sugarcane breeding are discussed.     

Assessment of Genetic Diversity in Upland Cotton (<Emphasis Type="Italic">Gossypium hirsutum</Emphasis> L.) Breeding Lines by using Amplified Fragment Length Polymorphism (AFLP) Markers and Morphological Characteristics

Genetic diversity in 24 advanced breeding lines of cotton was studied by using six amplified fragment length polymorphism (AFLP) primer-pairs and 14 morphological characters. The six selected AFLP primer-pairs generated a total of 535 amplification products, of which 460 were found to be polymorphic resulting in 85.9% polymorphism. The observed genetic distances using AFLP markers ranged from 30% to 87% with an average of 34%. A wide range of variability was observed for all the morphological traits studied. The range in taxonomic distance was from 0.60 to 2.77. Most of the lines could be clustered in two major clusters in both the analyses. But the correlation coefficient between the pair-wise distances estimated from AFLPs and the average taxonomic distances estimated from morphological characters was found to be 0.04. UPGMA cluster analysis revealed inconsistencies in the clustering patterns, as the co-phenetic correlation coefficient between the dendrograms for morphological and AFLP data indicated a poor fit for the two data types. From combined information, genotypes ‘RST-12’, ‘H 1226’, ‘P 348’, ‘KDCAKD’, ‘CISV 24’ and ‘H1222’ were found to be distinct from rest of the material.