Sanjeet Kumar

Genetic diversity in Capsicum germplasm based on microsatellite and random amplified microsatellite polymorphism markers.

A sound knowledge of the genetic diversity among germplasm is vital for strategic germplasm collection, maintenance, conservation and utilisation. Genomic simple sequence repeats (SSRs) and random amplified microsatellite polymorphism (RAMPO) markers were used to analyse diversity and relationships among 48 pepper (Capsicum spp.) genotypes originating from nine countries. These genotypes covered 4 species including 13 germplasm accessions, 30 improved lines of 4 domesticated species and 5 landraces derived from natural interspecific crosses. Out of 106 SSR markers, 25 polymorphic SSR markers (24xa0%) detected a total of 76 alleles (average, 3.04; range, 2–5). The average polymorphic information content (PIC) was 0.69 (range, 0.29–0.92). Seventeen RAMPO markers produced 87 polymorphic fragments with average PIC of 0.63 (range, 0.44–0.81). Dendrograms based on SSRs and RAMPOs generated two clusters. All 38 Capsicum annuum genotypes and an interspecific landrace clustered together, whereas nine non-annuum (three Capsicum frutescens, one Capsicum chinense, one Capsicum baccatum and four interspecific landraces) genotypes clustered separately. Genetic variation within non-annuum genotypes was greater than the C. annuum genotypes. Distinctness of interspecific derivative landraces grown in northeast India was validated; natural crossing between sympatric Capsicum species has been proposed as the mechanism of their origin.

The okra (Abelmoschus esculentus) transcriptome as a source for gene sequence information and molecular markers for diversity analysis.

A combined leaf and pod transcriptome of okra (Abelmoschus esculentus (L.) Moench) has been produced by RNA sequencing and short read assembly. More than 150,000 unigenes were obtained, comprising some 46 million base pairs of sequence information. More than 55% of the unigenes were annotated through sequence comparison with databases. The okra transcriptome sequences were mined for simple sequence repeat (SSR) markers. From 935 non-redundant SSR motifs identified in the unigene set, 199 were chosen for testing in a germplasm set, resulting in 161 polymorphic SSR markers. From this set, 19 markers were selected for a diversity analysis on 65 okra accessions comprising three different species, revealing 58 different genotypes and resulted in clustering of the accessions according to species and geographic origin. The okra gene sequence information and the marker resource are made available to the research community for functional genomics and breeding research.

Virus Diseases of Peppers (Capsicum spp.) and Their Control

The number of virus species infecting pepper (Capsicum spp.) crops and their incidences has increased considerably over the past 30 years, particularly in tropical and subtropical pepper production systems. This is probably due to a combination of factors, including the expansion and intensification of pepper cultivation in these regions, the increased volume and speed of global trade of fresh produce (including peppers) carrying viruses and vectors to new locations, and perhaps climate change expanding the geographic range suitable for the viruses and vectors. With the increased incidences of diverse virus species comes increased incidences of coinfection with two or more virus species in the same plant. There is then greater chance of synergistic interactions between virus species, increasing symptom severity and weakening host resistance, as well as the opportunity for genetic recombination and component exchange and a possible increase in aggressiveness, virulence, and transmissibility. The main virus groups infecting peppers are transmitted by aphids, whiteflies, or thrips, and a feature of many populations of these vector groups is that they can develop resistance to some of the commonly used insecticides relatively quickly. This, coupled with the increasing concern over the impact of over- or misuse of insecticides on the environment, growers, and consumers, means that there should be less reliance on insecticides to control the vectors of viruses infecting pepper crops. To improve the durability of pepper crop protection measures, there should be a shift away from the broadscale use of insecticides and the use of single, major gene resistance to viruses. Instead, integrated and pragmatic virus control measures should be sought that combine (1) cultural practices that reduce sources of virus inoculum and decrease the rate of spread of viruliferous vectors into the pepper crop, (2) synthetic insecticides, which should be used judiciously and only when the plants are young and most susceptible to infection, (3) appropriate natural products and biocontrol agents to induce resistance in the plants, affect the behavior of the vector insects, or augment the local populations of parasites or predators of the virus vectors, and (4) polygenic resistances against viruses and vector insects with pyramided single-gene virus resistances to improve resistance durability.

QTL mapping for important horticultural traits in pepper (Capsicum annuum L.)

Quantitative trait loci (QTLs) for plant height (PHT) and other yield-related traits including number of fruits per plant (NFP), ten fruits weight (TFW), fruit length (FL), fruit width (FW), total fruit weight (ToFW) and pericarp thickness (PT) were mapped in intraspecific advanced recombinant inbred line (RIL) populations of pepper. The RILs were evaluated for 2xa0years (F8 and F9) for plant height and seven other yield-related traits. Three types of molecular markers; simple sequence repeat (SSR), sequenced characterized amplified region (SCAR) and random amplified polymorphic DNA (RAPD)—were used to generate linkage maps. A total of 10 QTLs for yield-related traits were mapped on four linkage groups (LG). QTLs for plant height were mapped on LG5. The phenotypic contribution of these QTLs ranged from 8xa0% to 51xa0% in mean over environments. Out of 10 QTLs detected, nine were stable in both environments except the QTL for fruit length (Qfl.iivr.3.4) on LG3. The five QTLs; Qfw.iivr-2.1, Qtfw.iivr-2.1, Qtofw.iivr-2.1, Qnfp.iivr-2.1 and Qpt.iivr-2.1 were on the same marker interval on LG2 and one QTL, Qtofw.iivr-3.1 were tightly linked on LG3, which suggests that these genomic regions play an important role in enhancing pepper production. The genomic regions of all stable QTLs identified may serve as potential target regions for fine mapping and development of molecular markers for manipulation of yield and morphological traits in pepper.

Phenotypic and genotypic responses of chili (Capsicum annuum L.) progressive lines with different resistant genes against anthracnose pathogen (Colletotrichum spp.)

Anthracnose disease caused by Colletotrichum spp. is a serious disease of chili (Capsicum annuum), particularly in tropical countries. Host plant resistance breeding is one of the most effective disease management strategies. It requires identification of parents with genes resistant to Colletotrichum species predominant in a given region. For phenotypic evaluation, 35 chili lines consisting of progressive lines of C. annuum derived from C. baccatum PBC80 (34 lines) and from C. chinense PBC932 (one line) were inoculated with two aggressive isolates of Colletotrichum acutatum (Ca) and C. capsici (Cc) by injection into the pericarp of green and red-ripe fruit. Lesion diameters were scored atxa0seven days after inoculation. Two simple sequence repeat (SSR) and one sequence characterized amplified region (SCAR) markers were used for validation in four progressive lines and three each of susceptible and resistant checks for genotypic response. The progressive lines were classified into 10 groups based on their responses to two pathogens and at the two fruit stages. Four progressive lines (101, 205, 210 and 215) were selected and used for developing crosses to combine resistance genes from two sources resistant to Ca and Cc at both fruit stages. Progressive lines derived from PBC80 showed DNA fragment 231xa0bp amplified by primer HpmsE032 associated with Cc at green fruit stages. Hence the HpmsE032 marker could be considered useful in the selection of resistant genotypes derived from PBC80.

Molecular Markers Associated to Two Non-allelic Genic Male Sterility Genes in Peppers (Capsicum annuum L.)

Male sterility is of high importance in hybrid seed production of hot and sweet peppers. Genic (or nuclear) male sterility (GMS) is a simply inherited (usually monogenic recessive) and highly stable trait. However, one major disadvantage of using GMS is 1:1 segregation of male sterile to male fertile plants in every subsequent generation. Molecular markers tightly linked to genic male sterility (ms) genes would facilitate an efficient and rapid transfer of ms genes into different genetic backgrounds through marker-assisted backcrossing. The two non-allelic genic male sterility genes ms3 and msw in hot and sweet pepper backgrounds, respectively, are monogenic recessive. Genotyping by sequencing (GBS) in an F2 population segregating for ms3 gene in hot pepper and in an F6 inbred near-isogenic line (NIL) population segregating for msw gene in sweet pepper yielded 9,713 and 7,453 single nucleotide polymorphism markers, respectively. Four candidate SNPs co-segregating with ms3 gene and one co-segregating with msw gene were identified by bulk segregant analysis and physically mapped to chromosomes 1 and 5, respectively. In hot pepper, two markers [HPGMS2 (CAPS) and HPGMS3 (dCAPS)] located 3.83 cM away from the ms3 gene and in sweet pepper the dCAPS marker SPGMS1 co-segregated (completely linked) with the msw gene were developed. These markers will increase the efficacy of the male sterility genes for pepper breeding, as they can be useful in developing the genic male sterile lines in parental inbred lines of commercial hybrids through marker-assisted backcrossing, hybrid seed production, and genetic purity testing of hybrid seeds.