Mapping novel QTLs for yield related traits from a popular rice hybrid KRH-2 derived doubled haploid (DH) population.

A doubled haploid (DH) population consisting of 125 DHLs derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R) was utilized for Quantitative Trait Loci (QTL) mapping to identify novel genomic regions associated with yield related traits. A genetic map was constructed with 126 polymorphic SSR and EST derived markers, which were distributed across rice genome. QTL analysis using inclusive composite interval mapping (ICIM) method identified a total of 24 major and minor effect QTLs. Among them, twelve major effect QTLs were identified for days to fifty percent flowering (qDFF12-1), total grain yield/plant (qYLD3-1 and qYLD6-1), test (1,000) grain weight (qTGW6-1 and qTGW7-1), panicle weight (qPW9-1), plant height (qPH12-1), flag leaf length (qFLL6-1), flag leaf width (qFLW4-1), panicle length (qPL3-1 and qPL6-1) and biomass (qBM4-1), explaining 29.95-56.75% of the phenotypic variability with LOD scores range of 2.72-16.51. Chromosomal regions with gene clusters were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1) and on chromosome 6 for total grain yield/plant (qYLD6-1), flag leaf length (qFLL6-1) and panicle length (qPL6-1). Majority of the QTLs identified were observed to be co-localized with the previously reported QTL regions. Five novel, major effect QTLs associated with panicle weight (qPW9-1), plant height (qPH12-1), flag leaf width (qFLW4-1), panicle length (qPL3-1) and biomass (qBM4-1) and three novel minor effect QTLs for panicle weight (qPW3-1 and qPW8-1) and fertile grains per panicle (qFGP5-1) were identified. These QTLs can be used in breeding programs aimed to yield improvement after their validation in alternative populations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-03045-7.

Molecular mapping of QTLs for yield related traits in recombinant inbred line (RIL) population derived from the popular rice hybrid KRH-2 and their validation through SNP genotyping.

The study was undertaken to identify the quantitative trait loci (QTLs) governing yield and its related traits using a recombinant inbred line (RIL) population derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R). A genetic map spanning 294.2 cM was constructed with 126 simple sequence repeats (SSR) loci uniformly distributed across the rice genome. QTL analysis using phenotyping and genotyping information identified a total of 22 QTLs. Of these, five major effect QTLs were identified for the following traits: total grain yield/plant (qYLD3-1), panicle weight (qPW3-1), plant height (qPH12-1), flag leaf width (qFLW4-1) and panicle length (qPL3-1), explaining 20.23-22.76% of the phenotypic variance with LOD scores range of 6.5-10.59. Few genomic regions controlling several traits (QTL hotspot) were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1). Significant epistatic interactions were also observed for total grain yield per plant (YLD) and panicle length (PL). While most of these QTLs were observed to be co-localized with the previously reported QTL regions, a novel, major QTL associated with panicle length (qPL3-1) was also identified. SNP genotyping of selected high and low yielding RILs and their QTL mapping with 1,082 SNPs validated most of the QTLs identified through SSR genotyping. This facilitated the identification of novel major effect QTLs with much better resolution and precision. In-silico analysis of novel QTLs revealed the biological functions of the putative candidate gene (s) associated with selected traits. Most of the high-yielding RILs possessing the major yield related QTLs were identified to be complete restorers, indicating their possible utilization in development of superior rice hybrids.

Characterization of a new antifungal lipid transfer protein from wheat.

Lipid transfer proteins (LTPs) are members of the family of pathogenesis-related proteins (PR-14) that are believed to be involved in plant defense responses. In this study, a novel gene Ltp 3F1 encoding an antifungal protein from wheat (Sumai 3) was subcloned, overexpressed in Escherichia coli BL-21 (DE3) and enriched using ammonium sulfate fractionation followed by gel permeation chromatography. Molecular phylogeny analyses of wheat Ltp 3F1 gene showed a strong identity to other plant LTPs. Predicted three-dimensional structural model showed the presence of 6 alpha-helices and 9 loop turns. The active site catalytic residues Gly30, Pro50, Ala52 and Cys55 may be suggested for catalyzing the reaction involved in lipid binding. SDS-PAGE analysis confirmed the production of recombinant fusion protein. The LTP fusion protein exhibited a broad-spectrum antifungal activity against Alternaria sp., Rhizoctonia solani, Curvularia lunata, Bipolaris oryzae, Cylindrocladium scoparium, Botrytis cinerea and Sarocladium oryzae. Gene cassette with cyanamide hydratase (cah) marker and Ltp 3F1 gene was constructed for genetic transformation in tobacco. Efficient regeneration was achieved in selective media amended with cyanamide. Transgenic plants with normal phenotype were obtained. Results of PCR and Southern, Northern and Western hybridization analyses confirmed the integration and expression of genes in transgenic plants. Experiments with detached leaves from transgenic tobacco expressing Ltp 3F1 gene showed fungal resistance. Due to the innate potential of broad-spectrum antifungal activity, wheat Ltp 3F1 gene can be used to enhance resistance against fungi in crop plants.

Simple and economical assay systems for evaluation of phosphinothricin resistant transgenics of sorghum, Sorghum bicolor. (L.) Moench., and pearl millet, Pennisetum glaucum (L.) R. Br.

Five simple and rapid methods for evaluation of sorghum and pearl millet transgenics resistant to herbicide phosphinothricin (used as selectable marker) were studied. For rapid in vitro selection, three assays (establishment of sensitivity curves for embryogenic calli, determination of lethal doses for seed germination, and a rapid screening of cut young leaves based on the colour change of the medium) were established. For rapid screening of transgenic progeny, effects of in vivo Basta leaf spray and dip tests were studied at three different morphological stages. For all the above assays, LD50, and LD100 values were higher for pearl millet than sorghum. However, in both the crops, genotype effect was not significant. The assays standardized in the study were found to be effective for rapid, economical and mass-scale identification and characterization of transgenic plants of sorghum and pearl millet.