Identification and analysis of gamma-irradiation-induced Stemphylium blight tolerant lentil (Lens culinaris) mutant.

In the short-season winter environment of India and Bangladesh, lentil growth and seed yield are significantly hindered by foliar blight caused by Stemphylium botryosum. As the international germplasm pool lacks a resistance source, the study aims to develop a mutant population to identify a high-yielding mutant resistance against the pathogen. A gamma-irradiated population was developed based on its GR50 dose of 248.8 Gy. The screening of almost 130,000 M2 plants identified a tolerant lentil mutant, MM216. The multi-location trials revealed that MM216 showed an impressive and robust resistance; the selected mutant line could be recommended as a donor in the lentil breeding program against the pathogen globally. A 100 g seed was exposed to a GR50 dose to develop the M1 population. At maturity, at least 100 M2 seeds of each 1300 M1 plant were harvested individually. So, almost 130,000 M2 plants were screened in the disease hot spot. The selected mutants were advanced to M7 by screening in the field and challenged in controlled conditions with the pure pathogen isolate. A resistance mutant, MM216, with a per cent disease index (PDI) of <10, was identified where the mean of the check varieties, WBL 77, was >55. The resistance ability was confirmed further in controlled conditions. The fungal and plant DNA ratio was almost negligible in the tolerant mutant, whereas it was 0.17 in WBL77 at 196 h post-inoculation. The selected mutant did not display any yield penalty, but there was a delay in flowering by a week compared to WBL77.

The Ratio of A400/A1800 Mapping Identifies Chromosomal Regions Containing Known Photoprotection Recovery-Related Genes in Rice.

The rice, like other plants, undergoes photoprotection mode by increasing nonphotochemical quenching (NPQ) in high light intensity (> 1200 µmol m- 2s- 1 PPFD), which attenuates photosystem II yield (φPSII) drastically. The plant remains in photoprotection mode even after light intensity becomes not stressful for an extended period. While there are significant differences in the time it takes for photoprotection to recover among different genotypes, its use is limited in plant breeding because measuring the chlorophyll fluorescence parameters in progressive actinic light after dark adaptation takes more than forty-five minutes per genotype. The study finds that instantly measured A400/A1800 ratio by five minutes in flag leaves of 25 diverse genotypes strongly associated with the φPSII400 differences between theoretical and actual, qPd400 and NPQ400 with R2 values 0.74, 0.65 and 0.60, respectively. In two consecutive years, GWAS of A400/A1800 ratio identified the regions with genes reported earlier for plant photoprotection recovery. Additionally, QTL analysis in a RIL population also identified the regions carrying known genes related to photoprotection. Thus, the A400/A1800 ratio can quickly phenotype many plants for easier introgression of the traits in popular cultivars. The identified genotypes, genes, and QTLs can be used to improve yield potential and allele mining.

A mis-splicing early flowering 3 (elf3) allele of lentil is associated with yield enhancement under terminal heat stress.

There is a vast scope of area expansion of lentils after harvesting wet rice in South Asia. However, due to the photoperiod effect and terminal heat, the existing short-duration varieties failed to minimize yield loss under late-sown conditions. A mis-splicing causing A/G SNP present in the last nucleotide of exon 3 of early flowering 3 (ELF3) gene (elf3 allele) in a lentil line, L4710, is associated with the photoperiod insensitive flowering and the fast absolute growth rate (AGR). None of the Indian cultivars tested in this study, either early or late, possesses the non-functional elf3 allele. However, the A to G transition in ELF3-exon2 replaces glycine with aspartic acid at the 403rd amino acid in all the Indian varieties tested, compared to the reference sequence of Mediterranean accession, ILL5588. Therefore, targeting A/G SNP of exon 3, a PCR-based codominant marker is developed. The elf3 allele is correlated with the fast AGR and early flowering, but low yield and biomass, in an L4710 × LL56-derived RIL-population, compared to ELF3 carrying alleles when sown on 15th November. However, in a month of delayed sowing (20th December), the same elf3-RILs revealed a higher yield and biomass with slower AGR Moreover, three elf3-carrying lines, grown in delayed condition (20 December) for two consecutive years in three locations, outyielded three popular high-yielding cultivars that carry functional ELF3. Thus, elf3-carrying high-yielding lines could be the breeder's choice to expand and enhance lentil yield in short-season environments and in vast rice fallows of south Asia, where delayed rice harvest occurs frequently.

Rice (Oryza sativa) alleviates photosynthesis and yield loss by limiting specific leaf weight under low light intensity.

The physiological mechanisms of shade tolerance and trait plasticity variations under shade remain poorly understood in rice (Oryza sativa L.). Twenty-five genotypes of rice were evaluated under open and shade conditions. Various parameters to identify variations in the plasticity of these traits in growth irradiance were measured. We found wide variations in specific leaf weight (SLW) and net assimilation rate measured at 400µmolm-2 s-1 photosynthetic photon flux density (PPFD; referred to as A 400 ) among the genotypes. Under shade, tolerant genotypes maintained a high rate of net photosynthesis by limiting specific leaf weight accompanied by increased intercellular CO2 concentration (C i ) compared with open-grown plants. On average, net photosynthesis was enhanced by 20% under shade, with a range of 2-30%. Increased accumulation of biomass under shade was observed, but it showed no correlation with photosynthetic plasticity. Chlorophyll a /b ratio also showed no association with photosynthetic rate and yield. Analysis of variance showed that 11%, 16%, and 37% of the total variance of A 400 , SLW, and C i were explained due to differences in growth irradiance. SLW and A 400 plasticity in growth irradiance was associated with yield loss alleviation with R 2 values of 0.37 and 0.16, respectively. Biomass accumulation was associated with yield loss alleviation under shade, but no correlation was observed between A 400 and leaf-N concentration. Thus, limiting specific leaf weight accompanied by increased C i rather than leaf nitrogen concentration might have allowed rice genotypes to maintain a high net photosynthesis rate per unit leaf area and high yield under shade.

Yield-enhancing SPIKE allele from the aus-subtype indica rice and its allele specific codominant marker.

Improving spikelet number without limiting panicle number is an important strategy to increase rice productivity. In this study, a spikelet number enhancing SPIKE-allele was identified from the aus subtype indica rice, cv. Bhutmuri, which has an identical japonica like corresponding sequence including a retrotransposon sequence, usually absent in indica genotypes, like IR64. An allele-specific singletube PCR-based codominant marker targeting an A/G single-nucleotide polymorphism (SNP) at the 3'UTR was identified for easier genotyping. The yield enhancing ability of the Bhutmuri-SPIKE allele carrying RILs and NILs over IR64-SPIKE allele carrying alleles was due to increased number of filled grains/panicle. More than three times higher abundance of SPIKE transcripts was observed in Bhutmuri and NILs carrying this allele compared with IR64 and its allele carrying NILs. Higher rate of photosynthesis at more than 900 µmolm-2s-1 light intensity and more than six small vascular bundles between the two large vascular bundles in the flag leaves of Bhutmuri and its allele carrying NILs were also observed. The identified SPIKE allele and the marker associated with it will be useful for increasing the productivity of rice by marker-assisted breeding.

Identification and analysis of low light tolerant rice genotypes in field conditions and their SSR-based diversity in various abiotic stress tolerant lines.

The yield potentiality of kharif rice is not completely used even under well-irrigated agro-ecosystem, mainly due to low irradiance by overcast cloud throughout the growing season in eastern India. We observed more than 50% yield reduction compared to the performance of 100 high-yield genotypes for consecutive three years both under open and 30-35% reduced light intensity, mainly by 34%, 25% and 12% reduction of panicle number, grains per panicle and test weight. As per the analysis of variance, genotypic variance explained 39% of the total yield-variation under shade with 58% heritability. Overall, the maintenance of equal panicle per plant in both open and shade has the highest association with shade tolerance. Purnendu, Sashi and Pantdhan19 showed less than 28% yield-reduction by maintenance or even by increasing grain numbers under shade and test weight. On the other hand, maintenance of an equal number of panicle under both situations was the key to the tolerance of Bhasamanik, Sasarang, Rudra and Swarnaprabha. As compared to open, we noticed the improvement of chlorophyll a and b under shade but saw a poor correlation with the shade tolerance index. Comparing the net photosynthesis rate (Pn) in eight genotypes, we found the best tolerant line ranked last with least Pn at low light intensity (400 µmol m-2 s-1). We also identified diverse parental combinations between newly identified shade tolerant and abiotic stress tolerant high-yielding rice lines following diversity analysis using 54 simple-sequence repeats. Thus, the selected tolerant lines from a large set of genotypes with different adjustment ability to keep up high yield under low light intensity can be used for physiological, molecular analysis as well as pyramiding of traits.