Because lignin limits the use of wood for fiber, chemical, and energy production, strategies for its downregulation are of considerable interest. We have produced transgenic aspen (Populus tremuloides Michx.) trees in which expression of a lignin biosynthetic pathway gene Pt4CL1 encoding 4-coumarate:coenzyme A ligase (4CL) has been downregulated by antisense inhibition. Trees with suppressed Pt4CL1 expression exhibited up to a 45% reduction of lignin, but this was compensated for by a 15% increase in cellulose. As a result, the total lignin–cellulose mass remained essentially unchanged. Leaf, root, and stem growth were substantially enhanced, and structural integrity was maintained both at the cellular and whole-plant levels in the transgenic lines. Our results indicate that lignin and cellulose deposition could be regulated in a compensatory fashion, which may contribute to metabolic flexibility and a growth advantage to sustain the long-term structural integrity of woody perennials.

Biotechnology on genetic control of lignin biosynthesis in trees -Repression of lignin biosynthesis promotes cellulose accumulation and growth in transgenic trees-

Background

The control of plant anthocyanin accumulation is via transcriptional regulation of the genes encoding the biosynthetic enzymes. A key activator appears to be an R2R3 MYB transcription factor. In apple fruit, skin anthocyanin levels are controlled by a gene called MYBA or MYB1, while the gene determining fruit flesh and foliage anthocyanin has been termed MYB10. In order to further understand tissue-specific anthocyanin regulation we have isolated orthologous MYB genes from all the commercially important rosaceous species.

Results

We use gene specific primers to show that the three MYB activators of apple anthocyanin (MYB10/MYB1/MYBA) are likely alleles of each other. MYB transcription factors, with high sequence identity to the apple gene were isolated from across the rosaceous family (e.g. apples, pears, plums, cherries, peaches, raspberries, rose, strawberry). Key identifying amino acid residues were found in both the DNA-binding and C-terminal domains of these MYBs. The expression of these MYB10 genes correlates with fruit and flower anthocyanin levels. Their function was tested in tobacco and strawberry. In tobacco, these MYBs were shown to induce the anthocyanin pathway when co-expressed with bHLHs, while over-expression of strawberry and apple genes in the crop of origin elevates anthocyanins.

Conclusions

This family-wide study of rosaceous R2R3 MYBs provides insight into the evolution of this plant trait. It has implications for the development of new coloured fruit and flowers, as well as aiding the understanding of temporal-spatial colour change.

An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae

Empirical threshold values for quantitative trait mapping.

Can we use entomopathogenic fungi as endophytes for dual biological control of insect pests and plant pathogens

Genomic selection (GS) is a promising approach exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. In plant breeding it provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost benefit balance was an important consideration for GS to work in crop plants. Availability of genome-wide high-throughput, cost effective and flexible markers, having low ascertainment bias, suitable for large population size as well for both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species. These factors were the major limitations to marker systems viz., SSR and array-based, and was unimaginable before the availability of next-generation sequencing (NGS) technologies which have provided novel SNP genotyping platforms especially the genotyping by sequencing (GBS). These marker technologies have changed the entire scenario of marker applications and made the use of GS a routine work for crop improvement in both model and non-model crop species. The NGS based genotyping have increased genomic-estimated breeding value (GEBV) prediction accuracies over other established marker platform in cereals and other crop species, and made dream of GS true in crop breeding. But to harness the true benefits from GS, these marker technologies will be combined with high-throughput phenotyping (HTP) for achieving the valuable genetic gain from complex traits. Moreover, the continuous decline in sequencing cost will make the WGS feasible and cost effective for GS in near future. Till that time matures the targeted sequencing seems to be more cost-effective option for large scale marker discovery and GS, particularly in case of large and un-decoded genomes.

/pdf/genomic-selection-in-the-era-of-next-generation-sequencing-40tt921czj.pdf

Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding.

As a term, “next generation plant breeding” is increasingly becoming popular in crop breeding programmes, conferences, scientific fora and social media (Schnable, 2013). Being a frontier area of crop science and business, it is gaining considerable interest among scientific community and policymakers and funds flow from entrepreneurs and research funding agencies. Plant breeding is a continuous attempt to alter genetic architecture of crop plants for efficient utilization as food, fodder, fiber, fuel or other end uses. Although the scientific concepts in plant breeding originated about 100 years ago, domestication and selection of desirable plants from prehistoric periods have contributed tremendously to ensure human food security (Gepts, 2004). During the past few decades, well supported crop improvement programmes for major crops started reaping benefits from cutting edge technologies of biological sciences, particularly in the form of molecular markers and transgenic crop development, which in combination with conventional phenotype based selection, defines the current generation plant breeding practices. Different types of molecular markers have been developed and extensively used during the last three decades for identifying linkage between genes and markers, discovering quantitative trait loci (QTLs), pyramiding desired genes and performing marker assisted foreground and background selections for introgression of desired traits (Varshney and Tuberosa, 2007). However, these markers are based mostly on electrophoretic separation of DNA fragments, which limits detection of genetic polymorphism. In large plant breeding populations, genotyping may take up several months depending on marker system, adding more cost to genotyping. The next generation plant breeding would thus demand more efficient technologies to develop low cost, high-throughput genotyping for screening large populations within a smaller time frame.

/pdf/next-generation-sequencing-technologies-for-next-generation-286ev926wz.pdf

Next generation sequencing technologies for next generation plant breeding.

https://cyberleninka.org/article/n/1097108.pdf

Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species

An experiment was conducted to introduce the entomopathogen Beauveria bassiana (Balsamo) Vuillemin (Ascomycota: Hypocreales) as an endophyte in jute (Corchorus olitorius), a bast fibre crop through seed treatment. Colonization of root, leaf, stem, capsule, and seed were assessed through plating on selective medium and PCR based detection using B. bassiana specific SCAR markers. Endophytic colonization was detected in all the plants grown from treated seeds, but all the plant parts were not colonized. Colonization was detected in leaves, stems, and green capsules but not in roots and seeds. The endophytic colonization was influenced by both plant part and sampling period. Colonization was greater in leaves (55.87%) compared to stems (12.53%) and capsules (42.44%). The percent colonization was higher in case of 60 days old plants (43.34%) than in 30 days (23.89%) and 120 days (35.39%) old plants. As B. bassiana has already been reported to be pathogenic on jute pests, namely semilooper (Anomis sabulifera) and bihar hairy caterpillar (Spilosoma obliqua), its season long endophytic colonization within jute plant suggests a novel approach of biological control of these pests through seed treatment with the entomopathogen.

Establishment of the fungal entomopathogen Beauveria bassiana as a season long endophyte in jute ( Corchorus olitorius ) and its rapid detection using SCAR marker

Beauveria bassiana (Balsamo) Vuillemin (Ascomycota: Hypocreales), an entomopathogenic fungus, was introduced through seed inoculation with spore suspension as an endophyte in white jute (Corchorus capsularis L.), a bast fiber crop. Out of nine B. bassiana strains, seven, viz., ITCC 6063, ITCC 4512, ITCC 4563, ITCC 5562, ITCC 4796, ITCC 5408 and ITCC 4705, became established as endophytes. The endophytic colonization was initially detected by cultivation on selective medium. Colonization was confirmed by polymerase chain reaction (PCR) using sequence characterized amplified region (SCAR) marker. Endophytic B. bassiana strains colonized in leaves of all the plants grown from treated seeds. However, the colonization frequency varied among the strains. The highest colonization frequency (70.09%) was recorded in ITCC 6063 followed by ITCC 5562 (67.67%) and ITCC 5408 (64.17%); ITCC 4512 exhibited the lowest (42.54%) colonization. ITCC 4925 and ITCC 4644 did not show any colonization. Endophytic colonization of B. bassiana reduced stem weevil infestation under pot culture. ITCC 5408 and ITCC 6063 were found most efficient, with only 10.44% and 14.06% infested plants, respectively.

Endophytic colonization of white jute ( Corchorus capsularis ) plants by different Beauveria bassiana strains for managing stem weevil ( Apion corchori )

We generated the bast transcriptomes of a deficient lignified phloem fibre mutant and its wild-type jute (Corchorus capsularis) using Illumina paired-end sequencing. A total of 34,163 wild-type and 29,463 mutant unigenes, with average lengths of 1442 and 1136 bp, respectively, were assembled de novo, ~77-79 % of which were functionally annotated. These annotated unigenes were assigned to COG (~37-40 %) and GO (~22-28 %) classifications and mapped to 189 KEGG pathways (~19-21 %). We discovered 38 and 43 isoforms of 16 and 10 genes of the upstream shikimate-aromatic amino acid and downstream monolignol biosynthetic pathways, respectively, rendered their sequence similarities, confirmed the identities of 22 of these candidate gene families by phylogenetic analyses and reconstructed the pathway leading to lignin biosynthesis in jute fibres. We also identified major genes and bast-related transcription factors involved in secondary cell wall (SCW) formation. The quantitative RT-PCRs revealed that phenylalanine ammonia-lyase 1 (CcPAL1) was co-down-regulated with several genes of the upstream shikimate pathway in mutant bast tissues at an early growth stage, although its expression relapsed to the normal level at the later growth stage. However, cinnamyl alcohol dehydrogenase 7 (CcCAD7) was strongly down-regulated in mutant bast tissues irrespective of growth stages. CcCAD7 disruption at an early growth stage was accompanied by co-up-regulation of SCW-specific genes cellulose synthase A7 (CcCesA7) and fasciclin-like arabinogalactan 6 (CcFLA6), which was predicted to be involved in coordinating the S-layers' deposition in the xylan-type jute fibres. Our results identified CAD as a promising target for developing low-lignin jute fibres using genomics-assisted molecular approaches.

Pratik Satya

Papers

Next generation sequencing technologies for next generation plant breeding.

Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species

Establishment of the fungal entomopathogen Beauveria bassiana as a season long endophyte in jute ( Corchorus olitorius ) and its rapid detection using SCAR marker

Endophytic colonization of white jute ( Corchorus capsularis ) plants by different Beauveria bassiana strains for managing stem weevil ( Apion corchori )

Pathways associated with lignin biosynthesis in lignomaniac jute fibres