Characterization of Indian and exotic quality protein maize (QPM) and normal maize (Zea mays L.) inbreds using simple sequence repeat (SSR) markers

Polymorphism analysis and genetic diversity of normal maize and quality protein maize (QPM) inbreds among locally well adapted germplasm is a prerequisite for hybrid maize breeding program. The diversity analyses of 48 maize accessions including Indian and exotic germplasm using 75 simple sequence repeat (SSR) markers yielded 258 scorable alleles, out of which 251 alleles were polymorphic with an average of 3.35 alleles per locus. The polymorphism information content (PIC) values of all the polymorphic primers across the maize genotypes varied from 0.11 to 0.91, with an average value of 0.56. Di-nucleated repeats showed more number of average alleles (4.2) with more mean PIC value (0.61) than tri-, tetra-, penta- and hexa- nucleotide repeats. Gene diversity (He) was in the range of 0.11 (umc1766) to 0.81 (mmc0371 and bnlg1600) with an average value of 0.59, while heterozygosity (Ho) was observed with an average of 0.19, ranging from 0.02 (umc1495) to 0.98 (umc1906). Inbreeding coefficient (F) varied from 0.06 (umc2075) to 1.00 (15 SSR loci). Thus, the present study resulted to the identification of highly polymorphic SSR loci mmc0371, umc2364, umc1568, bnlg1600, phi026, umc2071 and bnlg1904 by considering the parameters of PIC value (≥0.74), gene diversity (≥0.75), inbreeding coefficient (≥0.62) and polymorphic alleles (≥4). These 7 polymorphic primers can be effectively used in a molecular breeding programs and quantitative trait loci (QTL) mapping studies since they exhibited very high polymorphism over other loci. Genotype pairs VQL 2 and CML 173 was observed to serve as ideal parents for mapping modifiers since they differ significantly for tryptophan content and also showed lowest similarity of 27% between them. Among all the genotypes, V 370 and B 06-7 (22%), V 25 and CM 152 (22%) and V 341 and CM 145 (24%) genotype pairs can be used in maize hybrid breeding programs for producing high yielding hybrids.Key words: Quality protein maize (QPM), gene diversity, heterozygosity, inbreeding coefficient, SSR markers, allele frequency

Development and molecular characterization of genic molecular markers for grain protein and calcium content in finger millet (Eleusine coracana (L.) Gaertn.)

Finger millet (Eleusine coracana (L.) Gaertn), holds immense agricultural and economic importance for its high nutraceuticals quality. Finger millets seeds are rich source of calcium and its proteins are good source of essential amino acids. In the present study, we developed 36 EST-SSR primers for the opaque2 modifiers and 20 anchored-SSR primers for calcium transporters and calmodulin for analysis of the genetic diversity of 103 finger millet genotypes for grain protein and calcium contents. Out of the 36 opaque2 modifiers primers, 15 were found polymorphic and were used for the diversity analysis. The highest PIC value was observed with the primer FMO2E33 (0.26), while the lowest was observed FMO2E27 (0.023) with an average value of 0.17. The gene diversity was highest for the primer FMO2E33 (0.33), however it was lowest for FMO2E27 (0.024) at average value of 0.29. The percentage polymorphism shown by opaque2 modifiers primers was 68.23 %. The diversity analysis by calcium transporters and calmodulin based anchored SSR loci revealed that the highest PIC was observed with the primer FMCA8 (0.30) and the lowest was observed for FMCA5 (0.023) with an average value of 0.18. The highest gene diversity was observed for primer FMCA8 (0.37), while lowest for FMCA5 (0.024) at an average of 0.21. The opaque2 modifiers specific EST-SSRs could able to differentiate the finger millet genotypes into high, medium and low protein containing genotypes. However, calcium dependent candidate gene based EST-SSRs could broadly differentiate the genotypes based on the calcium content with a few exceptions. A significant negative correlation between calcium and protein content was observed. The present study resulted in identification of highly polymorphic primers (FMO2E30, FMO2E33, FMO2-18 and FMO2-14) based on the parameters such as percentage of polymorphism, PIC values, gene diversity and number of alleles

Cross-genera transferability of rice and finger millet genomic SSRs to barnyard millet (Echinochloa spp.)

Barnyard millet (Echinochloa spp.) is an important crop from nutritional point of view, nevertheless, the genetic information is very scarce. In the present investigation, rice and finger millet genomic SSRs were used for assessing cross transferability, identification of polymorphic markers, syntenic regions, genetic diversity and population structure analysis of barnyard millet genotypes. We observed 100% cross transferability for finger millet SSRs, of which 91% were polymorphic, while 71% of rice markers were cross transferable with 48% polymorphic out of them. Twenty-nine and sixteen highly polymorphic finger millet and rice SSRs yielded a mean of 4.3 and 3.38 alleles per locus in barnyard millet genotypes, respectively. The PIC values varied from 0.27 to 0.73 at an average of 0.54 for finger millet SSRs, whereas it was from 0.15 to 0.67 at an average of 0.44 for rice SSRs. High synteny was observed for markers related to panicle length, yield-related traits, spikelet fertility, plant height, root traits, leaf senescence, blast and brown plant hopper resistance. Although the rice SSRs located on chromosome 10 followed by chromosome 6 and 11 were found to be more transferable to barnyard millet, the finger millet SSRs were more polymorphic and transferable to barnyard millet genotypes. These SSR data of finger millet and rice individually as well as combined together grouped the 11 barnyard millet genotypes into 2 major clusters. The results of population structure analysis were similar to cluster analysis

Nutraceutical value of finger millet (Eleusine coracana (L.) Gaertn.), and their improvement using omics approaches

The science of nutritional biology has progressed extensively over the last decade to develop food-based nutraceuticals as a form of highly personalized medicine or therapeutic agent. Finger millet [Eleusine coracana (L.) Gaertn.] is a crop with potentially tremendous but under-explored source of nutraceutical properties as compared to other regularly consumed cereals. In the era of growing divide and drawback of nutritional security, these characteristics must be harnessed to develop finger millet as a novel functional food. In addition, introgression of these traits into other staple crops can improve the well-being of the general population on a global scale. The objective of this review is to emphasize the importance of biofortification of finger millet in context of universal health and nutritional crisis. We have specifically highlighted the role that recent biotechnological advancements have to offer for enrichment of its nutritional value and how these developments can commission to the field of nutritional biology by opening new avenues for future research

Application of maize genomic SSR markers to identify the cross transferable, polymorphic markers and orthologous regions for finger millet genomics

627-634The vast amount of genetic information of maize crop gives a lot of scope for enriching the finger millet genomics research. There were very few genomic SSRs available in finger millet which was a major hurdle for the crop improvement. Hence, in the present study, we screened 271 maize genomic SSRs to identify the cross transferable, polymorphic SSRs, orthologous regions and for genetic diversity analysis in finger millet. Out of the 271 SSRs, 134 (49.4%) showed transferability and only 24 (18%) were found polymorphic. Seven markers were polymorphic between the genotypes VR708 and GPU48, whereas six markers were between GE86 and PRM801 genotypes which can be used in mapping populations and in comparative maps. The study also identified few putative orthologous regions for the genes like Zein alpha protein 1 (ZP1), golden 2 plant 2 gene (G2) and coloured aleurone gene. These 24 polymorphic SSRs yielded 61 scorable alleles with a mean of 2.37 alleles per locus. The polymorphism information content (PIC) varied from 0.14 to 0.69 at an average of 0.33, gene diversity was varied from 0.15 to 0.74 with an average value of 0.39, whereas heterozygosity observed with an average of 0.46 and ranged from 0.00 to 1.00 which showed a wide range of heterozygosity. The dendrogram generated from Power Marker V3.25 software grouped the finger millet genotypes into two major clusters based on the races. The markers identified in the study can be further use for linkage maps, comparative maps between maize and finger millet and for QTL mapping studies

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Not AvailableSingle nucleotide polymorphisms (SNPs) represent stable, bi-allelic nucleotide variations that are distributed throughout the genome and are the most abundant genetic variation. The present study targeted SNP related molecular differentiation and phylogenetic relationship of Indian Helicoverpa armigera populations by using expressed sequence tags (ESTs) of partial cytochrome oxidase subunit I (COI). The phylogenetic evaluation clearly separated the northern and southern Indian populations of H. armigera with little admixtures of central Indian populations. The SNP mining also revealed two major clusters as that of phylogeny with a total of 11 potential SNPs, of which 10 were in reliable haplotypes. The potential SNPs were found to contain eight transitions, three transversions and no indels (insertions and deletions). Out of 38 sequences, 13 were haplotypes in which 4 were single haplotypes. In cluster 1, the reliable bi-allelic SNPs were observed at 97, 166 and 265 nucleotide positions; while they were at 411, 423, 522, 655 and 656 positions in cluster 2. The present study highlighted the genetic polymorphism and relationship of Indian H. armigera, besides confirming the long distance migration and gene flow between the geographic populations.Not Availabl

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Not AvailableSeventy seven cassava genotypes along with three check varieties were employed for assessment of genetic variability, heritability and genetic gain during the period from 2015 to 2016 at, Horticultural Research Station, Dr. Y.S.R. Horticultural University, Venkataramannagudem, Andhra Pradesh under All India Co-ordinated research Project on Tuber crops. Analysis of variance revealed significant differences between genotypes for sixteen quantitative characters. Higher magnitude of PCV and GCV were observed for total leaf area, number of leaves per plant, HCN content, post-harvest physiological deterioration and tuber yield per hectare indicating the existence of wide range of genetic variability in the germplasm for these traits. High heritability estimates coupled with high estimates from genetic gain as per cent of means were observed for number of leaves per plant, plant height, HCN content and moderate heritability estimates coupled with high estimates from genetic gain as per cent of means were observed for petiole length, tuber dry matter content, tuber length, post-harvest physiological deterioration and tuber yield per hectare indicated that these characters were least influenced by the environmental effects and these characters were governed by additive genes and selection will be rewarding for improvement of such traits.Not Availabl

Mapping QTLs for opaque2 modifiers influencing the tryptophan content in quality protein maize using genomic and candidate gene-based SSRs of lysine and tryptophan metabolic pathway

Not AvailableKey message The mapping analysis resulted in identification of five significant QTLs for opaque2 modifiers influencing the tryptophan content in quality protein maize using functional and genomic SSR markers. Abstract Quality protein maize (QPM) was developed by selecting genetic modifiers that convert opaque2 mutant containing high lysine and tryptophan. There are several unlinked opaque2 modifier loci (Opm) in QPM whose location, nature and mode of action are not clear. To identify these Opm QTLs, we developed a population of 218 F2:3 individuals from a cross between VQL2 and VQL8, two isogenic QPM inbreds significantly differing in tryptophan content. Based on the data of the F2:3 population, five significant QTLs on chromosomes 5, 7 and 9 with LOD values more than 2.5 were identified and together explained 38.6 % of the total phenotypic variance (R2). The Wx1 gene which has influence on the amino acid composition of the maize endosperm was mapped on chromosome 9 near the marker phi022 and also validated by bulk analysis. The QTL near the SSR marker ZmASK3,developed from the aspartate kinase 2 gene of the lysine pathway, mapped on chromosome 5 and had LOD of 2.7 with R2 of 5.1 %. On chromosome 9, the QTL between the loci umc1430 and bnlg1401 had an LOD of 4.5 with R2 of 9.1 %, whereas the QTL between the loci bnlg1401 and phi022 had an LOD of 4.2 with R2 of 8.4 %. The third QTL was observed to be close to the marker umc2207 with an LOD of 4.8 and R2 of 8.4 %. The identified QTLs will be very useful in the marker-assisted back-cross breeding and transgressive breeding for the development of QPM maize.Not Availabl

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Not AvailableAllele identification for agro-morphological traits and stress resistance is a major concern across the globe for improving productivity of finger millet. Here, we used 46 genomic and 58 genic simple sequence repeats (SSRs) markers in a set of 66 accessions used to constitute a global mini-core collection for analysing their genetic structure as a population and establishing association among markers and twenty morphological traits including resistance to finger blast. Phenotypic data revealed a wide range of variation for all traits except flag leaf width and flag leaf sheath width. We got amplification of 81 alleles by the 31 genomic SSRs at an average of 2.61 alleles per locus. Polymorphism information content (PIC) values varied from 0.21 to 0.75 and average gene diversity was 0.49. Structure analysis of the population using the genomic SSR data divided the accessions into two clusters where Indian and exotic accessions were grouped in separate clusters. Genic SSRs which were associated with blast resistance genes, amplified 36 alleles at an average of 2 alleles per locus. PIC values ranged from 0.32 to 0.37 and average gene diversity was 0.45. Population structure analysis using data from these SSRs grouped the accessions into three clusters, which broadly correspond to their reaction to blast disease. Twenty-two significant associations were found using the GLM approach for 20 agro-morphological traits both in 2012 and 2014, while, 7 and 5 significant marker-trait associations were identified using MLM in 2012 and 2014 respectively. The SSR markers FMBLEST35 and FMBLEST36 designed from the Pi21 gene sequence of rice were found to be associated with blast disease resistance in finger millet indicating that the gene homologues play a significant role in an important role for neck blast resistance.Not Availabl

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Not AvailableAnomala dimidiata, a key white grub species associated with substantial crop losses in Indian Himalayan region, belong to one of the largest genera under scarab tribe, Anomalini. This paper presents the molecular variation and phylogenetic relationship of this species from the region using partial cytochrome oxidase I (COI) and cytochrome b (cyt b) sequences of mitochondrial genome in both nucleotides and polypeptides. The COI sequences were compared with available five sequences of A. dimidiata and 12 sequences of species under genus Anomala to study the divergence within and between species, respectively. However, cyt b sequence, as we were presenting for the first time, was compared with cyt b sequences of Drosophila yakuba whose entire mitochondrial genome was known and Dasylepida ishigakiensis, a scarabid white grub species, whose partial cyt b sequence is available. Both the genes were A + T biased and showed differential codon usage between species and geographical isolates. This is evidenced by discrepancies between nucleotide and deduced polypeptide sequences. The phylogenetic relationship of COI sequences also revealed that A. dimidata was evolutionarily associated with A. xanthoptera. The evolutionary distances of three cyt b sequences showed that differences were larger than expected based on evolutionary divergence. The study illustrates a complex genetic variation coupled with highly structured evolutionary divergences between and within species of Anomala.Not Availabl