Introgression of Drought Tolerance into Elite Basmati Rice Variety through Marker-Assisted Backcrossing

Drought is one of the major abiotic threat to rice production in the context of climate change.Super Basmati is an elite,fine grain basmati rice variety grown in Punjab,Pakistan.Due to drought sensitive in nature,its yield has been facing an alarming situation in production because of gradual decrease in irrigated water for a couple of years.Three reported novel QTLs for drought tolerance were selected for incorporation into Super Basmati by employing marker assisted selection strategy.IR55419-04 with novel QTLs was used as a donor parent.Foreground selection was performed by applying PCR based QTL linked SSR markers followed by recombinant selection by using 2-4 flanking markers.Background selection was exercised by using polymorphic SSR markers for maximum genome recovery of the Super Basmati.The individuals homozygous at the target QTLs and with maximum background of Super Basmati at the rest of the non-target genome was selected for evaluation of drought tolerance.Under drought stress conditions,the yields of all introgressed lines(ILs)were 44.2%-125.7%higher than recurrent parent.Six superior ILs that are drought tolerant and very similar to Super Basmati in terms of agronomic and grain quality traits are marked for release as drought-tolerant varieties in arid regions or for use in breeding programs of high grain quality and drought-tolerant parents.

Drought-responsive genes expressed predominantly in root tissues are enriched with homotypic cis-regulatory clusters in promoters of major cereal crops

The root appears to be the most relevant organ for breeding drought stress tolerance.However, our knowledge about temporal and spatial regulation of drought-associated genes in the root remains fragmented, especially in crop plants. We performed a meta-analysis of expression divergence of essential drought-inducible genes and analyzed their association with cis-elements in model crops and major cereal crops. Our analysis of42 selected drought-inducible genes revealed that these are expressed primarily in roots,followed by shoot, leaf, and inflorescence tissues, especially in wheat. Quantitative real-time RT-PCR analysis confirmed higher expression of TaDREB2 and TaAQP7 in roots,correlated with extensive rooting and drought-stress tolerance in wheat. A promoter scan up to 2 kb upstream of the translation start site using phylogenetic footprinting revealed708 transcription factor binding sites, including drought response elements(DREs), auxin response elements(Aux REs), MYCREs/MYBREs, ABAREs, and ERD1 in 19 selected genes.Interestingly, these elements were organized into clusters of overlapping transcription factor binding sites known as homotypic clusters(HCTs), which modulate drought physiology in plants. Taken together, these results revealed the expression preeminence of major drought-inducible genes in the root, suggesting its crucial role in drought adaptation. The occurrence of HCTs in drought-inducible genes highlights the putative evolutionary modifications of crop plants in developing drought adaptation. We propose that these DNA motifs can be used as molecular markers for breeding drought-resilient cultivars, particularly in the cereal crops.

Exploitation of Concatenated Olive Plastome DNA Markers for Reliable Varietal Identification for On-Farm Genetic Resource Conservation

Rapid and reliable identification of olive plants using DNA markers has been attempted in the past but the selection of polymorphic regions for discrimination at varietal level remained obscure. Recent sequencing of plastid genome of the olive flaunts high resolution Cp markers for olive DNA fingerprinting. Using this information, we designed a combination of chloroplast markers to amplify genes recruited in photosynthesis, ribosomal and NADH energy metabolism for varietal identification of olive plants. Concatenated DNA sequences of more than 100 unknown and 10 reference plants samples were analyzed using various bioinformatics and phylogenetic tools. Conserved blocks of nucleotide sequences were detected in multiple alignments. Phylogenetic reconstruction differentiated the unknown plants into various clusters with known varieties. Further narrowing down of the samples through UPGMA tree clearly separated the plants into Arbosana, Frantoio and Koroneiki as the major varieties. Multiple alignments of these clusters revealed important variety specific SNPs including G and T nucleotides at specific positions. Sequence identifying at intra cultivar level was more than 98.79% while it dropped to 97%, and even to 96% at inter varietal level. Furthermore, a neighbor net network analysis separated these three clusters, thus validating the results of UPGMA tree. Over all, out of 100 plants samples, 49 plants were identified that fall into 10 varieties including Arbosana, Carolea, Chetoui, Coratina, Domat, Frantoio, Gemlik, Koroneiki,Leccino and Moraiolo. The maximum number of known plants belongs to Frantoio and Gemlik (8 each). The least number of samples was identified from Carolea, Domat and Moraiolo with 2 samples each. However, 51 plants could not be identified, as plants were not clustered with any of reference control. Our results have implications in on-farm conservation of olive germplasm and provision of genuine material for multiplication of authentic varieties. This strategy can be extended to varietal identification of other plant species.