Germplasm variability-assisted near infrared reflectance spectroscopy chemometrics to develop multi-trait robust prediction models in rice.

Rice is a major staple food across the world in which wide variations in nutrient composition are reported. Rice improvement programs need germplasm accessions with extreme values for any nutritional trait. Near infrared reflectance spectroscopy (NIRS) uses electromagnetic radiations in the NIR region to rapidly measure the biochemical composition of food and agricultural products. NIRS prediction models provide a rapid assessment tool but their applicability is limited by the sample diversity, used for developing them. NIRS spectral variability was used to select a diverse sample set of 180 accessions, and reference data were generated using association of analytical chemists and standard methods. Different spectral pre-processing (up to fourth-order derivatization), scatter corrections (SNV-DT, MSC), and regression methods (partial least square, modified partial least square, and principle component regression) were employed for each trait. Best-fit models for total protein, starch, amylose, dietary fiber, and oil content were selected based on high RSQ, RPD with low SEP(C) in external validation. All the prediction models had ratio of prediction to deviation (RPD) > 2 amongst which the best models were obtained for dietary fiber and protein with R 2 = 0.945 and 0.917, SEP(C) = 0.069 and 0.329, and RPD = 3.62 and 3.46. A paired sample t-test at a 95% confidence interval was performed to ensure that the difference in predicted and laboratory values was non-significant.

Genome wide identification and characterization of microsatellite markers in black pepper (Piper nigrum): A valuable resource for boosting genomics applications.

Black pepper is one of the most valued and widely used spices in the world and dominates multi-billion dollar global spices trade. India is amongst the major producers, consumers and exporters of black pepper. In spite of its commercial and cultural importance, black pepper has received meagre attention in terms of generation of genomic resources. Availability of markers distributed throughout the genome would facilitate and accelerate genetic studies, QTL identification, genetic enhancement and crop improvement in black pepper. In this perspective, the sequence information from the recently sequenced black pepper (Piper nigrum) genome has been used for identification and characterisation of Simple Sequence Repeats (SSRs). Total 69,126 SSRs were identified from assembled genomic sequence of P. nigrum. The SSR frequency was 158 per MB making it, one SSR for every 6.3 kb in the assembled genome. Among the different types of microsatellite repeat motifs, dinucleotides were the most abundant (48.6%), followed by trinucleotide (23.7%) and compound repeats (20.62%). A set of 85 SSRs were used for validation, of which 74 produced amplification products of expected size. Genetic diversity of 30 black pepper accessions using 50 SSRs revealed four distinct clusters. Further, the cross species transferability of the SSRs was checked in nine other Piper species. Out of 50 SSRs used, 19 and 31 SSRs were amplified in nine and seven species, respectively. Thus the identified SSRs may have application in other species of the genus Piper where genome sequence is not available yet. Present study reports the first NGS based genomic SSRs in black pepper and thus constitute a valuable resource for a whole fleet of applications in genetics and plant breeding studies such as genetic map construction, QTL identification, map-based gene cloning, marker-assisted selection and evolutionary studies in Piper nigrum and related species.

Cytotaxonomical analysis of Momordica L. (Cucurbitaceae) species of Indian occurrence.

Somatic chromosome number and detailed karyotype analysis were carried out in six Indian Momordica species viz. M. balsamina, M. charantia, M. cochinchinensis, M. dioica, M. sahyadrica and M. cymbalaria (syn. Luffa cymbalaria; a taxon of controversial taxonomic identity). The somatic chromosome number 2n = 22 was reconfirmed in monoecious species (M. balsamina and M. charantia). Out of four dioecious species, the chromosome number was reconfirmed in M. cochinchinensis (2n = 28), M. dioica (2n = 28) and M. subangulata subsp. renigera (2n = 56), while in M. sahyadrica (2n = 28) somatic chromosome number was reported for the first time. A new chromosome number of 2n = 18 was reported in M. cymbalaria against its previous reports of 2n = 16, 22. The karyotype analysis of all the species revealed significant numerical and structural variations of chromosomes. It was possible to distinguish chromosomes of M. cymbalaria from other Momordica species and also between monoecious and dioecious taxa of the genus. Morphology and crossability among the dioecious species was also studied. Evidence from morphology, crossability, pollen viability and chromosome synapsis suggests a segmental allopolyploid origin for M. subangulata subsp. renigera. The taxonomic status of the controversial taxon M. cymbalaria was also discussed using morphological, karyological and crossability data.