Sclerotinia stem rot caused by Sclerotinia sclerotiorum is a major disease of crop brassicas, with inadequate variation for resistance in primary gene pools. We utilized a wild Brassicaceae species with excellent resistance against stem rot to develop a set of B. juncea - B. fruticulosa introgression lines (ILs). These were assessed for resistance using a highly reproducible stem inoculation technique against a virulent pathogen isolate. Over 40% of ILs showed higher levels of resistance. IL-43, IL-175, IL-215, IL-223 and IL-277 were most resistant ILs over three crop seasons. Sequence reads (21x) from the three most diverse ILs were then used to create B. juncea pseudomolecules, by replacing SNPs of reference B. juncea with those of re-sequenced ILs. Genotyping by sequencing (GBS) was also carried out for 88 ILs. Resultant sequence tags were then mapped on to the B. juncea pseudomolecules, and SNP genotypes prepared for each IL. Genome wide association studies helped to map resistance responses to stem rot. A total of 13 significant loci were identified on seven B. juncea chromosomes (A01, A03, A04, A05, A08, A09 and B05). Annotation of the genomic region around identified SNPs allowed identification of 20 candidate genes belonging to major disease resistance protein families, including TIR-NBS-LRR class, Chitinase, Malectin/receptor-like protein kinase, defensin-like (DEFL), desulfoglucosinolate sulfotransferase protein and lipoxygenase. A majority of the significant SNPs could be validated using whole genome sequences (21x) from five advanced generation lines being bred for Sclerotinia resistance as compared to three susceptible B. juncea germplasm lines. Our findings not only provide critical new understanding of the defensive pathway of B. fruticulosa resistance, but will also enable development of marker candidates for assisted transfer of introgressed resistant loci in to agronomically superior cultivars of crop Brassica.

The capsid-coding (P1) and 3A regions of foot-and-mouth disease virus (FMDV) type A field isolates including two vaccine strains collected during 1977-2000 were analyzed. In the phylogenies, the isolates were distributed into two previously identified genotypes VI and VII, with multiple sub-genotypes that are temporally clustered. Comparison of the antigenic relationships of field isolates with the two vaccine strains (IND 17/77 and IND 490/97) and the reference strains of the genotypes VI (IND 233/99) and VII (IND 40/00) indicated two broad antigenic groups that correlate with the phylogenetic groupings (genotypes VI and VII), and are highly divergent from the vaccine strains. The maximum likelihood method of selection analysis identified a number of amino acid sites within the P1 region to be under weak positive selection. Some of the positively selected sites were mapped at/near the antigenically critical amino acid sites of the P1 region, indicating host immune pressure as one of the important driving force behind the observed genetic and antigenic diversity in FMDV. A small number of selected sites are located in the heparan sulphate-binding pocket of the virus, suggesting a fitness advantage for cell entry of the virus. No positive selection was detected in the 3A dataset.

Background: Guava (Psidium guajava L.) is an important fruit crop of tropical and subtropical areas of the world. Genomics resources in guava are scanty. RNA-Seq based tissue specific expressed genomic information, de novo transcriptome assembly, functional annotation and differential expression among contrasting genotypes has a potential to set the stage for the functional genomics for traits of commerce like colored flesh and apple color peel. Results: Development of fruit from flower involves orchestration of myriad molecular switches. We did comparative transcriptome sequencing on leaf, flower and fruit tissues of cv. Allahabad Safeda to understand important genes and pathways controlling fruit development. Tissue specific RNA sequencing and de novo transcriptome assembly using Trinity pipeline provided us the first reference transcriptome for guava consisting of 84,206 genes comprising 279,792 total transcripts with a N50 of 3603 bp. Blast2GO assigned annotation to 116,629 transcripts and PFam based HMM profile annotated 140,061 transcripts with protein domains. Differential expression with EdgeR identified 3033 genes in Allahabad Safeda tissues. Mapping the differentially expressed transcripts over molecular pathways indicate significant Ethylene and Abscisic acid hormonal changes and secondary metabolites, carbohydrate metabolism and fruit softening related gene transcripts during fruit development, maturation and ripening. Differential expression analysis among colored tissue comparisons in 3 cultivars Allahabad Safeda, Punjab Pink and Apple Color identified 68 candidate genes that might be controlling color development in guava fruit. Comparisons of red vs green peel in Apple Color, white pulp vs red pulp in Punjab Pink and fruit maturation vs ripening in non-colored Allahabad Safeda indicates up-regulation of ethylene biosynthesis accompanied to secondary metabolism like phenylpropanoid and monolignol pathways.

Thalassemia and thalassemic hemoglobinopathies pose serious health problem leading to severe morbidity and mortality in Indian population. Plethora of hemoglobin variants is prevalent in multiethnic Indian population. The aim of the present study was to analyze laboratory aspects, namely, hematological profile and HPLC findings of the hemoglobin variants detected, and to discuss problems that we faced in diagnosis in a routine clinical laboratory. We screened a total of 4800 cases in a hospital based population of North India in a 2-years period of by automated HPLC method using the Variant Hemoglobin Testing System (Variant II Beta Thalassemia Short Program, Bio-Rad Laboratories) under the experimental conditions specified by the manufacturer. Whole blood in EDTA was used and red cell indices were determined using automated hematology analyzer. We detected 290 cases with abnormal variants in which beta thalassemia was the most common followed by hemoglobin E. Here, we discuss the laboratory aspects of various hemoglobin disorders and diagnostic difficulties in cases like borderline HbA2 values, presence of silent mutation, alpha thalassemia gene, and few rare variants which at times require correlation with genetic study. Special attention was given to HbA2 level even in presence of a structural variant to rule out coinheritance of beta thalassemia gene.

Timely transition to flowering, maturity and plant height are important for agronomic adaptation and productivity of Indian mustard (B. juncea), which is a major edible oilseed crop of low input ecologies in Indian subcontinent. Breeding manipulation for these traits is difficult because of the involvement of multiple interacting genetic and environmental factors. Here, we report a genetic analysis of these traits using a population comprising 92 diverse genotypes of mustard. These genotypes were evaluated under deficient (N75), normal (N100) or excess (N125) conditions of nitrogen (N) application. Lower N availability induced early flowering and maturity in most genotypes, while high N conditions delayed both. A genotyping-by-sequencing approach helped to identify 406,888 SNP markers and undertake genome wide association studies (GWAS). 282 significant marker-trait associations (MTA's) were identified. We detected strong interactions between GWAS loci and nitrogen levels. Though some trait associated SNPs were detected repeatedly across fertility gradients, majority were identified under deficient or normal levels of N applications. Annotation of the genomic region (s) within ± 50 kb of the peak SNPs facilitated prediction of 30 candidate genes belonging to light perception, circadian, floral meristem identity, flowering regulation, gibberellic acid pathways and plant development. These included over one copy each of AGL24, AP1, FVE, FRI, GID1A and GNC. FLC and CO were predicted on chromosomes A02 and B08 respectively. CDF1, CO, FLC, AGL24, GNC and FAF2 appeared to influence the variation for plant height. Our findings may help in improving phenotypic plasticity of mustard across fertility gradients through marker-assisted breeding strategies.

The present study aimed to measure amniotic fluid index (AFI) in high-risk pregnancies at C30 weeks of gestation and its correlation with fetal growth and perinatal outcome. The Study was carried out in the Department of Obstetrics and Gynecology Hindu Rao Hospital, Delhi. Ultrasound examination was done on women with highrisk pregnancy (pregnancy-induced hypertension, intrauterine growth restriction, diabetes, and postdated pregnancy etc.) attending the antenatal OPD and maternity ward at C30 weeks of gestation. AFI was measured by the four quadrant technique. The study included 48 (48 %) primigravida and 52 (52 %) multigravida. Sixteen patients with a history of previous abortion had mean AFI of 9.97 cm which was lower than patients with no history of previous abortion i.e., 11.87 cm (P C 0.1 insignificant). The mean AFI was maximum between 34-36 weeks, i.e., 13.1 cm, after which, it gradually decreased to 9.08 cm beyond 40 weeks. Mean AFI of patients with \40 weeks of gestation gradually decreased from 12.2 cm to 8.0 cm after 42 weeks (P value \0.05). Patients with IUGR had low mean AFI i.e., 9.8 cm whereas mean AFI in patients without IUGR was 12.1 cm (P value \0.01). Congenital anomalies were found in 4 % patients in the present study. Out of seven cases of perinatal mortality encountered, four (57 %) had abnormal AFI values, of which, two had low AFI (i.e., \8 cm) and two had abnormally-high AFI values i.e., [18 cm. Serious congenital malformations were present in three neonates, which resulted in early neonatal death. Out of these three, one patient had low AFI i.e., \8 cm and one had abnormally-high AFI value i.e., [24 cm. The study supports the view that AFI is a quick, noninvasive, and good indicator of fetal outcome in high-risk pregnancy.

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