Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh].

BACKGROUND: Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping. RESULTS: In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥ 18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. CONCLUSION: We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus Cajanus. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea.

The insect upper lip (labrum) is a nonsegmental appendage-like structure.

The insect upper lip--the labrum--is a lobe-like structure anterior to the mouth opening. Whether the labrum represents a fused pair of segmental appendages or evolved independently is heavily debated. Here, we identify additional similarities of the regulatory gene network active in labrum and trunk appendages. However, we do not find a labral parasegment boundary and we show that labral Tc-Dll expression is independent of Tc-wg and Tc-hh signals. In contrast, Tc-Dll expression in all trunk appendages does require these signals. Finally, we identify crucial differences between the location of the labrum and trunk appendages: the labrum develops in median rather than lateral tissues and is part of an anterior nonsegmental tissue marked by and dependent on Tc-six3 activity. To reconcile these seeming contradictory results, we propose that the genetic network evolved in either labrum or trunk appendages and became redeployed at a novel location to form the other structure.

Mating compatibility among helicoverpa armigera (Lepidoptera: Noctuidae) occurring on selected host plants and Bt cotton survivors.

Helicoverpa armigera (Hiibner) (Lepidoptera: Noctuidae) is a well-known polyphagous insect pest. Mating compatibility among the insects occurring on different host plants is essential for free gene flow among populations. We tested the extent of crossability and fecundity of the insects that survived on Bacillus thuringiensis (Bt) cotton with those occurring on pigeon pea, Cajanus cajun (L.) Millsp., non-Bt cotton, Gossypium hirsutum L.; sunflower, Helianthus annuus; sorghum, Sorghum bicolor L. Moench.; okra, Abelmoschus moschatus Medikus; chickpea, Cicer arietinum L.; marigold, Tagetes spp.; and tomato, Lycopersicum esculentum L., crops. The insects from different crops were freely crossable with those collected from Bt cotton and among themselves. The average fecundity across different crosses ranged from 314.1 to 426.3 in direct and from 305.8 to 421.7 eggs per female in reciprocal crosses. In any given cross, a minimum of 85.89% egg hatch was recorded. Furthermore, the F1 individuals of different cross combinations were found to cross freely with their parents (BC1) and among themselves with similar fecundity and egg hatch. High crossability among H. armigera occurring on different host plants suggests that crop mosaics that may exist in countries such as India could play an important role as natural, nonstructured refugia and prolong the durability of the genes deployed for controlling this insect.