Genetic variability parameters and correlation among 11 quantitative traits were studied in 219 soybean working collection during kharif 2014-15 at Bengaluru. Analysis of variance revealed ...significant differences among the 219 accessions for all the quantitative characters studied except for the seed size. Among the traits, number of clusters per pod exhibited highest estimate of phenotypic coefficient of variance (PCV) (37.04) and genotypic coefficient of variance (GCV) (36.94) followed by 100-seed weight (g) (PCV=31.96, GCV=31.46) and number of branches per plant (PCV=29.56, GCV=29.18). Heritability was highest (>70%) for all the characters studied. High heritability coupled with high genetic advance as per cent mean was recorded for plant height (cm), number of branches per plant, number of clusters per plant, number of pods per cluster, number of seeds per pod, pod length (cm), seed size (cm) and 100-seed weight (g). Hundred seed weight (g) exhibited highly significant and positive correlation with seed size (cm) (0.68) and pod length (cm) (0.17). A very wide range of variability was observed for 11 qualitative traits in the working collection and this can be potentially used for the improvement of soybean for yield and related traits.
•Identified 1859 genomic SSRs from 1091 scaffolds representing 60% of the whole genome sequence of cluster bean.•Validated 89 genomic SSRs using 54 cluster bean accessions and two wild relatives.•Tri ...and tetra-nucleotide repeat containing SSRs were more polymorphic while dinucleotide repeats were more abundant.•Genetic distance-based clustering analysis distinguished the wild relatives from C. tetragonoloba.
Cluster bean (Cyamopsis tetragonoloba), also known as guar, is an important industrial crop owing to its high gum content in the endosperm. Availability of sufficient genomic resources, especially, DNA markers, greatly aids genetic improvement of a crop. In this study, we identified 1859 genomic SSRs, for the first time, from 1091 scaffolds representing 60% of the cluster bean genome. Further we validated 89 of these markers using 54 cultivated guar accessions and two wild relatives, Cyamopsis serrata and Cyamopsis senegalensis. Seven SSRs were monomorphic even with the wild relatives while 11 were polymorphic only between species with 72 being polymorphic within C. tetragonoloba accessions. Polymorphism information content of the markers ranged from 0.017 to 0.62 with an average of 0.19. Cross-transferability rates of 62% observed for the genomic SSRs suggested divergence between the cultivated and the wild species. Genomic SSRs mined in this study though showed a high proportion of dinucleotide repeats (48.5%), while tri- and tetranucleotide repeats were found to be more polymorphic. Genetic diversity analysis of the 56 accessions using the 82 polymorphic markers could differentiate the cultivated accessions of C. tetragonoloba into four major clusters, two of which had two sub-clusters while the wild accessions formed a separate cluster. Since chromosome-wide distribution of the SSRs is unknown and genetic linkage maps in guar is not available, we used the soybean genome as a reference and identified 29 genome-wide and unlinked SSRs markers. Population structure analysis (PSA) using these markers revealed six subpopulations, more or less similar to the major and sub-clusters identified by the neighbor joining analysis. Further PSA identified an entry from subpopulation 6 to have admixture with the wild relatives. Annotation of the validated genomic SSR containing sequences using green plant nr protein database revealed that 16 of them were genic in nature. This is the first report on genomic SSRs and their utilization in unraveling the genetic diversity in cluster bean.
Tomato (Solanum lycopersicum L.) is high value crop, also called as protective food due to its high nutritional and biochemical compounds. Correlation and path analysis was carried out for 147 tomato ...recombinant inbred line population. Correlation studies suggested that the association of fruit yield per plant was positive and significant with plant height (0.595), branches per plant (0.657), fruits per cluster (0.500), clusters per plant (0.717), average fruit weight (0.244) and fruits per plant (0.891). Path analysis revealed that among eleven characters studied only two characters viz., average fruit weight (0.415) and fruits per plant (0.817) showed very high positive and direct effect on yield per plant. This study helps to understand the mutual relationship among various traits thereby assist in selecting the character contributing to the yield.
Pigeonpea Sterility Mosaic Disease (PSMD) is an important foliar disease caused by Pigeonpea sterility mosaic virus (PPSMV) which is transmitted by eriophyid mites (Aceria cajani Channabasavanna). In ...present study, a F2 mapping population comprising 325 individuals was developed by crossing PSMD susceptible genotype (Gullyal white) and PSMD resistant genotype (BSMR 736). We identified a set of 32 out of 300 short decamer random DNA markers that showed polymorphism between Gullyal white and BSMR 736 parents. Among them, eleven DNA markers showed polymorphism including coupling and repulsion phase type of polymorphism across the parents. Bulked Segregant Analysis (BSA), revealed that the DNA marker, IABTPPN7, produced a single coupling phase marker (IABTPPN7414) and a repulsion phase marker (IABTPPN7983) co-segregating with PSMD reaction. Screening of 325 F2 population using IABTPPN7 revealed that the repulsion phase marker, IABTPPN7983, was co-segregating with the PSMD responsive SV1 at a distance of 23.9 cM for Bidar PPSMV isolate. On the other hand, the coupling phase marker IABTPPN7414 did not show any linkage with PSMD resistance. Additionally, single marker analysis both IABTPPN7983 (P<0.0001) and IABTPPN 7414 (P<0.0001) recorded a significant association with the PSMD resistance and explained a phenotypic variance of 31 and 36% respectively in F2 population. The repulsion phase marker, IABTPPN7983, could be of use in Marker-Assisted Selection (MAS) in the PPSMV resistance breeding programmes of pigeonpea.
In sorghum, stay-green is an important target trait considered for improvement of post-flowering drought tolerance. Prediction and expression profiling of genes present in the introgressed QTL ...regions of the genome paveway for identification of candidate genes and proof of genetic basis. Physical location for stay-green QTLs on different chromosomes in sorghum genome was mapped and the length of the QTL intervals ranged from 1.8 to 2.5 Mbp. The stable QTLs were commonly detected at two different locations and across three different consecutive seasons in two different mapping populations. Using the ab initio approach three algorithms viz., FGENESH, GENSCAN and GENMARK and their combinations, a total of five genes viz.,
NSP
,
NAD
,
PHD
,
MADS
,
MLO
in QTL
qSTG1A
(1.82 Mbp), ten genes viz.,
IAA
,
SORBIDRAFT
,
CYP450
,
GAG/POL
,
PK
,
GENE X
,
UGTS
,
MTC
,
AGP16
,
VP25
in
qSTG2
(2.54 Mbp) and one gene,
SF CC1
in
qSTG3
(2.18 Mbp) was predicted as common ones on chromosomes 3 and 1. Structural features and protein annotations indicated their involvement in drought tolerance pathways as compared with genbank information at NCBI. Expression profiling of NILs based on the functional annotations, qRT-PCR assays indicated upheavals of predicted genes at 30 and 45 DAF in leaf tissues of q
STG
introgressed lines and significant difference between transcript levels of genes in different DAF as revealed by statistical analyses. Results indicated the potential of QTL pyramiding for the improving plant performance under adverse environmental conditions.
Carrot (
Daucus carota
L.) is acknowledged as a highly valuable vegetable crop. Despite having high demand, limited breeding efforts have been made to develop the varieties and hybrids suitable to ...wider climatic conditions due to improper characterization of the available germplasm. An accession panel (AP) consisting of 144 accessions of five different root colors representing Asiatic and Western gene pools collected from different parts of India was utilized in the present study. This diverse AP was used to assess the population structure and genetic diversity from 80 polymorphic DNA markers distributed throughout the genome. Population structure, neighbor-joining (NJ) tree, and principal coordinate analysis (PCoA)-based diversity assessment divided the AP into three subpopulations/clusters. Greater than ninety percent polymorphism and the higher average polymorphic information content (͂> 0.50) coupled with higher gene diversity (He) indicating the broad genetic base of the population. Moderate to high F
st
and gene flow (Nm) between the subpopulations revealed a moderate genetic differentiation among Indian carrot accessions owing to the highly outcrossing nature of carrot. Analysis of molecular variance (AMOVA) exhibited higher variation among individuals within the subpopulations (69.00%) or total populations (19.00%) than among the subpopulations (13%) as expected in the single
Daucu
s species used here. The information obtained in the study would benefit the carrot breeders to explore the genetic diversity of the Indian carrots in the carrot breeding program for widening the genetic base and multi-color target trait improvement.
The present investigation was carried out using 191genotypes as mini core collections of pigeonpea along with 5 check varieties to know the genetic diversity at molecular level. Significant variation ...was observed by the way of analysis of variance for nine characters viz., days to 50 % flowering, days to maturity, plant height, number of branches per plant, pod bearing length, number of pods per plant, number of seeds per pod, seed yield per plant and hundred seed weight. Molecular diversity using 18 polymorphic simple sequence repeat (SSR) markers divided genotypes into 15 clusters, of which ICP-11059 and AK-101 were solitary, indicating their distinctiveness among all genotypes. Similarly, BSMR-533, JKM-7, RVK-285, ICP-1126, ICP-348, ICP-6859 and ICP-7869 were found distinct among the genotypes. Geographical origin based diversity separated Indian and non Indian genotypes. The Un weighted Pair Group Method with Arithmetic mean (UPGMA) based dendrogram indicated distinctiveness of ICP-13633 and Bennur local, as they formed solitary cluster. The SSR marker CcM 602, as it could differentiate 4 genotypes at different base pair size can be used for identification and finger printing of genotypes.
Pigeonpea (Cajanus cajan), an important food legume crop in the semi-arid regions of the world and the second most important pulse crop in India, has an average crop productivity of 780 kg/ha. The ...relatively low crop yields may be attributed to non-availability of improved cultivars, poor crop husbandry and exposure to a number of biotic and abiotic stresses in pigeonpea growing regions. Narrow genetic diversity in cultivated germplasm has further hampered the effective utilization of conventional breeding as well as development and utilization of genomic tools, resulting in pigeonpea being often referred to as an ‘orphan crop legume'. To enable genomics-assisted breeding in this crop, the pigeonpea genomics initiative (PGI) was initiated in late 2006 with funding from Indian Council of Agricultural Research under the umbrella of Indo-US agricultural knowledge initiative, which was further expanded with financial support from the US National Science Foundation's Plant Genome Research Program and the Generation Challenge Program. As a result of the PGI, the last 3 years have witnessed significant progress in development of both genetic as well as genomic resources in this crop through effective collaborations and coordination of genomics activities across several institutes and countries. For instance, 25 mapping populations segregating for a number of biotic and abiotic stresses have been developed or are under development. An 11X-genome coverage bacterial artificial chromosome (BAC) library comprising of 69,120 clones have been developed of which 50,000 clones were end sequenced to generate 87,590 BAC-end sequences (BESs). About 10,000 expressed sequence tags (ESTs) from Sanger sequencing and ca. 2 million short ESTs by 454/FLX sequencing have been generated. A variety of molecular markers have been developed from BESs, microsatellite or simple sequence repeat (SSR)-enriched libraries and mining of ESTs and genomic amplicon sequencing. Of about 21,000 SSRs identified, 6,698 SSRs are under analysis along with 670 orthologous genes using a GoldenGate SNP (single nucleotide polymorphism) genotyping platform, with large scale SNP discovery using Solexa, a next generation sequencing technology, is in progress. Similarly a diversity array technology array comprising of ca. 15,000 features has been developed. In addition, >600 unique nucleotide binding site (NBS) domain containing members of the NBS-leucine rich repeat disease resistance homologs were cloned in pigeonpea; 960 BACs containing these sequences were identified by filter hybridization, BES physical maps developed using high information content fingerprinting. To enrich the genomic resources further, sequenced soybean genome is being analyzed to establish the anchor points between pigeonpea and soybean genomes. In addition, Solexa sequencing is being used to explore the feasibility of generating whole genome sequence. In summary, the collaborative efforts of several research groups under the umbrella of PGI are making significant progress in improving molecular tools in pigeonpea and should significantly benefit pigeonpea genetics and breeding. As these efforts come to fruition, and expanded (depending on funding), pigeonpea would move from an ‘orphan legume crop' to one where genomics-assisted breeding approaches for a sustainable crop improvement are routine.
Carnation (Dianthus caryophyllus L.) is one of the fifth most important ornamental species worldwide. Many desirable plant characteristics such as big size flower, adaptation to stress, and intra or ...interspecific hybridization capability are dependent on plant ploidy level. We optimized a quick flow cytometry method for DNA content determination in carnation accession samples that allowed a systematic evaluation of ploidy levels. To verify the actual ploidy levels, we counted chromosome numbers in the root tips of representative cultivar for each ploidy level. The relative nuclear DNA content was distributed into four kinds of discontinuous groups: 1.32 to 1.95 pg (group 1), 2.03 to 2.72 pg (group 2), 2.98 to 4.65 pg (group 3) and 5.33 pg (group 4) which might correspond to the following ploidy levels; diploid, triploid, tetraploid and hexaploid. The results showed that out of 60 carnation accessions, 33 were diploid, 5 were triploid, 21 were tetraploid and 1 was hexaploid.
Charcoal rot caused by
Macrophomina phaseolina is an economically important disease in sorghum grown during the post rainy season in India. Variations in random amplified polymorphic DNA (RAPD) ...polymorphisms, chlorate sensitivity and pathogenicity were studied among sorghum isolates of
M. phaseolina collected from different parts of India. RAPD data based on 14 random primers of Kit A and C (OPA and OPC) on 20 isolates showed a high degree of polymorphism (98.1%) in different isolates. UPGMA dendrogram on RAPD data produced 7 clusters at the level of 37% similarity. Isolates from the same locations showed a tendency to group closer, substantiating closer genetic relatedness. Sorghum infecting
Macrophomina isolates showed a mixed response for sensitivity to potassium chlorate (120
mM). Chlorate-resistant isolates were predominant (>65% of the isolates) over sensitive isolates. Chlorate-sensitive isolates were found to be genetically closer among them than the resistant ones. For the first time it was shown that chlorate sensitivity in
Macrophomina had some relations with charcoal rot severity in sorghum.
PDF
