Institutional Publications

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Functional allele of a MATE gene selected during domestication modulates seed color in chickpea
(John Wiley & Sons, 2024) Thakro, Virevol; Varshney, Nidhi; Malik, Naveen; Daware, Anurag; Srivastava, Rishi; Mohanty, Jitendra K; Basu, Udita; Narnoliya, Laxmi; Jha, Uday Chand; Tripathi, Shailesh; Tyagi, Akhilesh K.; Parida, Swarup K.
Seed color is one of the key target traits of domestication and artificial selection in chickpeas due to its implications on consumer preference and market value. The complex seed color trait has been well dissected in several crop species; however, the genetic mechanism underlying seed color variation in chickpea remains poorly understood. Here, we employed an integrated genomics strategy involving QTL mapping, high-density mapping, map-based cloning, association analysis, and molecular haplotyping in an inter-specific RIL mapping population, association panel, wild accessions, and introgression lines (ILs) of Cicer gene pool. This delineated a MATE gene, CaMATE23, encoding a Transparent Testa (TT) and its natural allele (8-bp insertion) and haplotype underlying a major QTL governing seed color on chickpea chromosome 4. Signatures of selective sweep and a strong purifying selection reflected that CaMATE23, especially its 8-bp insertion natural allelic variant, underwent selection during chickpea domestication. Functional investigations revealed that the 8-bp insertion containing the third cis-regulatory RY-motif element in the CaMATE23 promoter is critical for enhanced binding of CaFUSCA3 transcription factor, a key regulator of seed development and flavonoid biosynthesis, thereby affecting CaMATE23 expression and proanthocyanidin (PA) accumulation in the seed coat to impart varied seed color in chickpea. Consequently, overexpression of CaMATE23 in Arabidopsis tt12 mutant partially restored the seed color phenotype to brown pigmentation, ascertaining its functional role in PA accumulation in the seed coat. These findings shed new light on the seed color regulation and evolutionary history, and highlight the transcriptional regulation of CaMATE23 by CaFUSCA3 in modulating seed color in chickpea. The functionally relevant InDel variation, natural allele, and haplotype from CaMATE23 are vital for translational genomic research, including marker-assisted breeding, for developing chickpea cultivars with desirable seed color that appeal to consumers and meet global market demand.
Restructuring plant types for developing tailor-made crops
(John Wiley & Sons, 2023) Basu, Udita; Parida, Swarup K.
Plants have adapted to different environmental niches by fine-tuning the developmental factors working together to regulate traits. Variations in the developmental factors result in a wide range of quantitative variations in these traits that helped plants survive better. The major developmental pathways affecting plant architecture are also under the control of such pathways. Most notable are the CLAVATA-WUSCHEL pathway regulating shoot apical meristem fate, GID1-DELLA module influencing plant height and tillering, LAZY1-TAC1 module controlling branch/tiller angle, and the TFL1-FT determining the floral fate in plants. Allelic variants of these key regulators selected during domestication shaped the crops the way we know them today. There is immense yield potential in the “ideal plant architecture” of a crop. With the available genome editing techniques, possibilities are not restricted to naturally occurring variations. Using a transient reprogramming system, one can screen the effect of several developmental gene expressions in novel ecosystems to identify the best targets. We can use the plant's fine-tuning mechanism for customizing crops to specific environments. The process of crop domestication can be accelerated with a proper understanding of these developmental pathways. It is time to step forward towards the next-generation molecular breeding for restructuring plant types in crops ensuring yield stability.
Millets: genetic and genomic resources
(John Wiley & Sons, 2011) Dwivedi, Sangam; Upadhyaya, Hari; Senthilvel, Senapathy; Hash, Charles; Fukunaga, Kenji; Diao, Xiamin; Santra, Dipak; Baltensperger, David; Prasad, Manoj
all-grained millets, comprising ten annual grasses from the family Poaceae and grown for grain, contribute $13% of annual global cereal production. Some are widely grown, while cultivation of others is restricted. They differ in ploidy, genome size, and breeding system, but their grains are all highly nutritious. Their most common nonfood uses are in brewing and as livestock feeds. Millets are C4 plants adapted to marginal lands in hot, drought-prone arid and semiarid regions. Selection for plant phenology and architecture, panicle shape, spikelet structure and reduced shattering, seed dormancy, and seed coat hardness contributed to their domestication. Approximately 161,708 millet accessions are preserved in gene banks globally. These show exceptional diver- sity associated for phenology, photoperiod sensitivity, tolerance to abiotic stresses, resistance to biotic stresses, seed storability and shelf life, and specific grain characteristics associated with end user preferences. Contributions from wild relatives’ toward enhancing cultivated gene pools have been limited to pearl millet and foxtail millet. Core or minicore/reference collections have been used to identify new sources of biotic stress resistances and abiotic stress tolerances. Waxy mutants have been selected in barnyard millet, foxtail millet, and proso millet for specific food uses. Pearl millet hybrids and open pollinated varieties (OPVs) with high iron and zinc grain densities will soon be available in India. While no transgenic work has reached field level, DNA markers are routinely used to assess millets’ population structure and genetic diversity. Genetic maps of varying density are reported in finger millet, foxtail millet, pearl millet, proso millet, and tef. Major quantitative trait loci associated with resis- tance to downy mildew, rust, and blast and tolerance to terminal drought stress have been backcrossed into elite inbred pearl millet hybrid parents. Marker- assisted backcrossing has been used to improve downy mildew resistance in pearl millet. Cytoplasmic-genetic male sterility (CMS)–based hybrids of pearl millet are extensively cultivated, and CMS systems for foxtail millet are under development. An aligned genome sequence of foxtail millet will be released in the near future as this millet is closely related to several polyploid bioenergy grasses. This foxtail millet genome sequence is highly syntenic with those of rice, sorghum, and maize, which should allow comprehensive surveys of genetic diversity for identifying and conserving diversity in grass germplasm with bioenergy crop potential.

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