Biology subjects

Chaluvadi, S. R.

Publications and source records attributed to Chaluvadi, S. R..

2 recordsLinked to original sources

bioRxiv2020

Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum

Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum and Sorghum bicolor inbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ~1920 bin markers spanning ~875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genetics↗

bioRxiv2019

Exceptional subgenome stability and functional divergence in allotetraploid teff, the primary cereal crop in Ethiopia

Teff (Eragrostis tef) is a cornerstone of food security in the Horn of Africa, where it is prized for stress resilience, grain nutrition, and market value. Despite its overall importance to small-scale farmers and communities in Africa, teff suffers from low production compared to other cereals because of limited intensive selection and molecular breeding. Here we report a chromosome-scale genome assembly of allotetraploid teff (variety Dabbi) and patterns of subgenome dynamics. The teff genome contains two complete sets of homoeologous chromosomes, with most genes maintained as syntenic gene pairs. Through analyzing the history of transposable element activity, we estimate the teff polyploidy event occurred [~]1.1 million years ago (mya) and the two subgenomes diverged [~]5.0 mya. Despite this divergence, we detected no large-scale structural rearrangements, homoeologous exchanges, or bias gene loss, contrasting most other allopolyploid plant systems. The exceptional subgenome stability observed in teff may enable the ubiquitous and recurrent polyploidy within Chloridoideae, possibly contributing to the increased resilience and diversification of these grasses. The two teff subgenomes have partitioned their ancestral functions based on divergent expression patterns among homoeologous gene pairs across a diverse expression atlas. The most striking differences in homoeolog expression bias are observed during seed development and under abiotic stress, and thus may be related to agronomic traits. Together these genomic resources will be useful for accelerating breeding efforts of this underutilized grain crop and for acquiring fundamental insights into polyploid genome evolution.

plant biology↗