Molecular Breeding for Abiotic Stresses in Maize (Zea mays L.)

Abiotic constraints resulting from climate changes have widespread yield reducing effects on all field crops and therefore should receive high priority for crop breeding research. Conventional breeding has progressed a lot in building tolerant genotypes but abiotic stress tolerance breeding is limited by the complex nature of abiotic stress intensity, frequency, duration and timing, linkage drag of undesirable traits/genes with desirable traits; and transfer of favorable genes/alleles from diverse plant genetic resources limited by gene pool barriers giving molecular breeding a good option for breeding plant genotypes that can thrive in stress environments. Molecular breeding (MB) approaches viz., marker-assisted selection (MAS), marker-assisted backcrossing breeding (MABB), marker assisted recurrent selection (MARS) and genomic selection (GS) or genome wide selection (GWS) offer opportunities for plant breeders to develop high yielding maize cultivars with resilience to diseases in less time duration precisely. For complex traits (mainly abiotic stresses) where multiple QTLs control the expression, new strategies like marker assisted recurrent selection (MARS) and genomic selection (GS) are employed to increase precision and to reduce cost of phenotyping and time duration with disease resilience. This review discusses recent developments in molecular breeding for developing and improving abiotic stress resilience in field crops

Studies on drought tolerance in maize inbred lines using morphological and molecular approaches

A set of hundred homozygous maize inbred lines were analyzed for drought toleranceby studying twenty-four traits related to maturity, morphological, physiological, yield, quality and few root traits. Evaluation confirmed a wide range of variability revealing significant response of main effects (lines, irrigations and years and their respective digenic and trigenic interactions). These lines were subjected to different stress regimes over years leading to identification of fifteen elite lines which performed well under droughtstress showing inbuilt drought tolerance. A set of 32 SSR markers, having genome-wide coverage, were chosen for genotyping the inbred lines. These markers generated a total of 239 polymorphic alleles with an average of 7.47 alleles per locus. The minimum and maximum PIC value was 0.886 and 0.608 with a mean of 0.782. The coefficient of genetic dissimilarity ranged from 0.215 to 0.148. DARwin derived cluster analysis grouped 15 elite maize lines in three major clusters with five lines each in cluster-III and II and four lines in cluster-I with KDM-361A as root. Molecular diversity however, confirmed diverse genetic nature of six lines (KDM-372, KDM-343A, KDM-331, KDM-961, KDM-1051 and KDM-1156) showing drought tolerance. Exploitation of identified elite lines in a crossing program involving all possible combinations would help to develop hybrids with inbuilt mechanism to drought tolerance. Markers viz., umc -1766, umc-1478 and phi-061 recorded PIC >8 and alleles per locus more than 9 and therefore, discriminated the set of lines more efficiently. Genotyping data complemented by morpho- hysiological parameters were used to identify a number of pair-wise combinations for the development of mapping population segregating for drought tolerance and potential heterotic pairs for the development of drought tolerant hybrids.

Quantitative response of wheat to sowing dates and irrigation regimes using ceres-wheat model

An experiment was conducted at Punjab Agricultural University, Ludhiana during 2014–15 and 2015–16, keeping four sowing dates {25th Oct (D1), 10th Nov (D2), 25th Nov (D3) and 10th Dec (D4)} in main plots and five irrigation schedules {irrigation at 15 (FC15), 25 (FC25), 35 (FC35) and 45 (FC45) % depletion of soil moisture from field capacity (FC) and a conventional practice} in sub plots. The objective of the study was to evaluate the performance of CERES-Wheat model for simulating yield and water use under varying planting and soil moisture regimes. The simulated and observed grain yield was higher in D1, with irrigation applied at FC15 as compared to all other sowing date and irrigation regime combinations. Simulated grain yield decreased by 19% with delay in sowing from 25th October to 10th December because of 8% reduction in simulated crop evapotranspiration. Simulated evapotranspiration decreased by 16%, wheat grain yield by 23% and water productivity by 15% in drip irrigation at 45% depletion from field capacity as compared to drip irrigation at 15% of field capacity. It was further revealed that the model performed well in simulating the phenology, water use and yield of wheat

Studies on fungal leaf blight of ridge gourd [Luffa acutangula (L.) Roxb.] in Kashmir valley

An extensive survey conducted during 2004 and 2005 revealed that Didymella blight was prevalent in all ridge gourd (Luffa acutangula) growing areas of Kashmir valley with varied levels of incidence and intensity. The incidence and intensity on leaves ranged from 22.0 to 64.0 and 7.7 to 34.8 per cent, respectively. The incidence on fruits was 6.8 to 18.8 per cent. The fungus inciting the disease was identified as Didymella bryoniae (Aureswarld) Rehm (Anamorph Phoma cucurbitacearum (Foutrey) Sacardo) on the basis of its morphological and pathological characteristics. Disease infection on leaves and fruits resulted in leaf blight and fruit rot, respectively. Disease initially appeared on lower leaves as small circular, light brown spots with chlorotic halo ranging in size from 0.5 to 1.0 mm. With the passage of time spots enlarged (up to 83 mm size) , developed concentric rings at the centre and turned dark brown with greyish white centre. The spots then coalesced, causing yellowing and blighting of the entire leaf. Symptoms on fruit appeared as dark green, irregularly circular water-soaked spots which enlarged rapidly and caused black rot. Black fructifications i.e, pycnidia and pseudothecia of the causal pathogen, were observed on infected tissue of both leaf and fruit which imparted black colour to the latter. The disease in the field appeared in June and reached its maximum by the end of September. Maximum apparent infection rate of 0.1858 and 0.1826 unit/day in the field were observed during fifth week of July in 2004 and during second week of July in 2005, respectively. Weather factors viz., temperature, RH and rainfall were found positively correlated with the disease development in terms of infection rate (unit/day) with 69 per cent contribution by rainfall alone. Single spored cultures from ascospore and pycnidiospore on potato dextrose agar (PDA) produced pycnidia after 10 to 12 days of incubation at 24±10C under 12/12 hour alternate cycles of light and darkness, however, pseudothecia were altogether absent. The fungus required incubation period of 4 days to cause infection in the inoculated host plants, whereas, on detached leaf and fruit it took 2 to 3 days. The fungus was found pathogenic to all the eight cucurbit plant species tested viz., Cucumis sativus (cucumber), Lagenaria siceraria (bottle gourd), Cucumis melo (muskmelon), Citrullus lanatus (watermelon), Mamordicha charantia (bitter gourd), Cucurbita pepo (squash), Luffa cylindrica (sponge gourd) and Cucurbita pepo (pumpkin) besides its natural host Luffa acutangula (ridge gourd) both under natural and artificial inoculation conditions. The best growth and fructification of the fungus was observed on potato dextrose agar and corn meal agar media with pH 7.0 when incubated at 24 ± 1 0C. Spore germination was also best at this temperature and pH level. The pathogen perpetuated in the form of spores on seeds and plant debris stored indoors under ambient laboratory conditions as these produced viable spores through out the observation period of twelve months. It also perpetuated as a dormant mycelium on plant debris left on the soil surface in open, however, pathogen was unable to survive on plant debris buried 7.5 cm deep in soil. Carbendazim and chlorothalonil from systemic and non-systemic fungitoxicants, respectively, as well as Allium sativum from botanicals tested under in vitro conditions exhibited maximum inhibition in mycelial growth and spore germination of the test fungus. The treatments found most promising under in vitro studies, when tested as seed treatment and foliar spray, treatment combination carbendazim seed treatment together with foliar sprays of carbendazim proved superior in controlling the disease and also increasing the fruit yield

Image_4_Viral metatranscriptomic approach to study the diversity of virus(es) associated with Common Bean (Phaseolus vulgaris L.) in the North-Western Himalayan region of India.JPEG

Plant viruses are a major threat to legume production worldwide. In recent years, new virus strains have emerged with increasing frequencies in various legume cropping systems, which demands the development of cutting-edge virus surveillance techniques. In this study, we surveyed the common bean fields of Kashmir valley for virus infection using a total of 140 symptomatic and non-symptomatic leaf samples collected from different locations. The genetic diversity of viruses was examined by high-throughput sequencing (HTS) with three viruses being identified, namely, Bean Common Mosaic Virus (BCMV), Bean Common Mosaic Necrosis Virus (BCMNV), and Clover Yellow Vein Virus (ClYVV). BCMNV and ClYVV are new reports from India. De novo assembly of transcriptome constructed near-complete genomes of these viruses. RT-PCR results confirmed the presence of these viruses with an emerge incidence of 56. 4% for BCMV, 27.1% for BCMNV and 16.4 for ClYVV in the valley. Several samples were found to contain multiple virus infections with BCMV being the most predominant. Recombination events were detected in the genomes of BCMV and ClYVV, but not BCMNV. Phylogenetic and pairwise identity matrix evidence suggests viral import from multiple countries. Our results demonstrate that HTS followed by multiplex PCR assay is a simple, rapid, and reliable approach for simultaneous diagnosis of plant viruses.</p

Table_1_Viral metatranscriptomic approach to study the diversity of virus(es) associated with Common Bean (Phaseolus vulgaris L.) in the North-Western Himalayan region of India.DOCX

Plant viruses are a major threat to legume production worldwide. In recent years, new virus strains have emerged with increasing frequencies in various legume cropping systems, which demands the development of cutting-edge virus surveillance techniques. In this study, we surveyed the common bean fields of Kashmir valley for virus infection using a total of 140 symptomatic and non-symptomatic leaf samples collected from different locations. The genetic diversity of viruses was examined by high-throughput sequencing (HTS) with three viruses being identified, namely, Bean Common Mosaic Virus (BCMV), Bean Common Mosaic Necrosis Virus (BCMNV), and Clover Yellow Vein Virus (ClYVV). BCMNV and ClYVV are new reports from India. De novo assembly of transcriptome constructed near-complete genomes of these viruses. RT-PCR results confirmed the presence of these viruses with an emerge incidence of 56. 4% for BCMV, 27.1% for BCMNV and 16.4 for ClYVV in the valley. Several samples were found to contain multiple virus infections with BCMV being the most predominant. Recombination events were detected in the genomes of BCMV and ClYVV, but not BCMNV. Phylogenetic and pairwise identity matrix evidence suggests viral import from multiple countries. Our results demonstrate that HTS followed by multiplex PCR assay is a simple, rapid, and reliable approach for simultaneous diagnosis of plant viruses.</p

Image_1_Viral metatranscriptomic approach to study the diversity of virus(es) associated with Common Bean (Phaseolus vulgaris L.) in the North-Western Himalayan region of India.JPEG

Plant viruses are a major threat to legume production worldwide. In recent years, new virus strains have emerged with increasing frequencies in various legume cropping systems, which demands the development of cutting-edge virus surveillance techniques. In this study, we surveyed the common bean fields of Kashmir valley for virus infection using a total of 140 symptomatic and non-symptomatic leaf samples collected from different locations. The genetic diversity of viruses was examined by high-throughput sequencing (HTS) with three viruses being identified, namely, Bean Common Mosaic Virus (BCMV), Bean Common Mosaic Necrosis Virus (BCMNV), and Clover Yellow Vein Virus (ClYVV). BCMNV and ClYVV are new reports from India. De novo assembly of transcriptome constructed near-complete genomes of these viruses. RT-PCR results confirmed the presence of these viruses with an emerge incidence of 56. 4% for BCMV, 27.1% for BCMNV and 16.4 for ClYVV in the valley. Several samples were found to contain multiple virus infections with BCMV being the most predominant. Recombination events were detected in the genomes of BCMV and ClYVV, but not BCMNV. Phylogenetic and pairwise identity matrix evidence suggests viral import from multiple countries. Our results demonstrate that HTS followed by multiplex PCR assay is a simple, rapid, and reliable approach for simultaneous diagnosis of plant viruses.</p

Image_2_Viral metatranscriptomic approach to study the diversity of virus(es) associated with Common Bean (Phaseolus vulgaris L.) in the North-Western Himalayan region of India.JPEG

Plant viruses are a major threat to legume production worldwide. In recent years, new virus strains have emerged with increasing frequencies in various legume cropping systems, which demands the development of cutting-edge virus surveillance techniques. In this study, we surveyed the common bean fields of Kashmir valley for virus infection using a total of 140 symptomatic and non-symptomatic leaf samples collected from different locations. The genetic diversity of viruses was examined by high-throughput sequencing (HTS) with three viruses being identified, namely, Bean Common Mosaic Virus (BCMV), Bean Common Mosaic Necrosis Virus (BCMNV), and Clover Yellow Vein Virus (ClYVV). BCMNV and ClYVV are new reports from India. De novo assembly of transcriptome constructed near-complete genomes of these viruses. RT-PCR results confirmed the presence of these viruses with an emerge incidence of 56. 4% for BCMV, 27.1% for BCMNV and 16.4 for ClYVV in the valley. Several samples were found to contain multiple virus infections with BCMV being the most predominant. Recombination events were detected in the genomes of BCMV and ClYVV, but not BCMNV. Phylogenetic and pairwise identity matrix evidence suggests viral import from multiple countries. Our results demonstrate that HTS followed by multiplex PCR assay is a simple, rapid, and reliable approach for simultaneous diagnosis of plant viruses.</p

Image_3_Viral metatranscriptomic approach to study the diversity of virus(es) associated with Common Bean (Phaseolus vulgaris L.) in the North-Western Himalayan region of India.TIF

Plant viruses are a major threat to legume production worldwide. In recent years, new virus strains have emerged with increasing frequencies in various legume cropping systems, which demands the development of cutting-edge virus surveillance techniques. In this study, we surveyed the common bean fields of Kashmir valley for virus infection using a total of 140 symptomatic and non-symptomatic leaf samples collected from different locations. The genetic diversity of viruses was examined by high-throughput sequencing (HTS) with three viruses being identified, namely, Bean Common Mosaic Virus (BCMV), Bean Common Mosaic Necrosis Virus (BCMNV), and Clover Yellow Vein Virus (ClYVV). BCMNV and ClYVV are new reports from India. De novo assembly of transcriptome constructed near-complete genomes of these viruses. RT-PCR results confirmed the presence of these viruses with an emerge incidence of 56. 4% for BCMV, 27.1% for BCMNV and 16.4 for ClYVV in the valley. Several samples were found to contain multiple virus infections with BCMV being the most predominant. Recombination events were detected in the genomes of BCMV and ClYVV, but not BCMNV. Phylogenetic and pairwise identity matrix evidence suggests viral import from multiple countries. Our results demonstrate that HTS followed by multiplex PCR assay is a simple, rapid, and reliable approach for simultaneous diagnosis of plant viruses.</p

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