Research
South Dakota State University
Core Winter Wheat Breeding: Major focus of my program is developing high yielding, disease resistant winter wheat varieties with good end-use quality for South Dakota and the Norther Great Plains.
1. Hard red winter (HRW) wheat cultivar ‘Oahe’ was released by SDAES (8/2016). Oahe offers a combination of high yield with good test weight and moderate resistance to stripe rust, leaf rust, wheat streak mosaic virus, and Fusarium head blight.
2. Hard red winter (HRW) wheat cultivar ‘Thompson’ was released by SDAES (11/2017). Thompson is a high yielding taller semi-dwarf HRW variety adapted to central South Dakota with moderate resistance to leaf rust and stem rust and acceptable milling quality.
3. Hard red winter (HRW) wheat cultivar ‘Winner’ was released by SDAES (12/2019). Winner is semi-dwarf variety with unusually broad adaptation to the eastern half of the Northern Great Plains. Winner has medium height and medium maturity with higher yield potential, good baking quality, and moderate resistance to stem rust.
4. Hard red winter (HRW) wheat cultivar ‘Draper’ was released by SDAES (12/2019). Draper is a semi-dwarf variety with good straw strength and a limited target region, specifically western South Dakota. Draper has improved yield potential with average test weight, grain protein, and good milling and baking quality. It is resistant to soilborne mosaic virus.
Genetics & Genomics: Enhancing diversity in wheat crop and develop germplasm with novel sources of resistance to biotic and abiotic stresses.
Identified and characterized genomic regions for resistance against Tan spot, Spetoria Nodorum Blotch (SNB), Spot Blotch and Bacterial Leaf Streak (BLS) using GWAS (see publications).
Kansas State University
Genome sequence is central for systematic understanding wheat biology and provides a comprehensive foundation for breeding higher yielding, drought-tolerant and disease-resistant cultivars. Major food crops species (Rice Maize, soybean, sorghum) have been sequenced in last decade however this has not been achieved in wheat and barley precluded by the size and complexity of their genomes. Efforts are underway across the globe to develop integrated physical and genetic map of wheat from last five years as first significant step in sequencing the wheat genome. Our group is working on developing an integrated physical and genetic map of four chromosomes 3A, 1D, 4D, 6D of wheat. BAC based physical map are very valuable for cloning of economically important genes for understanding the mechanism of their function. Resources developed under our projects have used in fine mapping and cloning of 2 genes/QTLs and are being used for several more genes.
Developing sequence-ready integrated genetic and physical map of four chromosomes of bread wheat: Leading the effort in developing sequence-ready physical maps CS 1D, 4D, 6D (project website) and 3A (project website) by fingerprinting ~500,000 BACs from chromosome- or chromosome arm-specific BAC libraries (see our database) and assembling them into BAC contigs.
Developed thousands of SNPs markers from next generation sequence analysis. Physically anchored thousands of EST-STS, SSR, SNPs markers on individual BACs and fingerprint contigs using multidimensional BAC pools. Ordering BAC contigs on the genetic maps developed using Illumina Golden Gate and Genotype By Sequencing (GBS) which would lead to BAC by BAC sequencing of four wheat chromosomes. In addition 10,000 BAC were end sequenced to develop over 1,400 chromosome specific markers for chromosome 3AS (see publications).
More than 100 agro-economic genes/QTls (see Figure) have been mapped on these chromosomes and physical maps is being used for fine mapping and cloning of several important genes like Pre-harvest sprouting, earliness per se, leaf rust resistance see publications) in several labs including WGRC.
Sequenced flow sorted chromosome 3A and selected clones from 3A MTP for comparative genomics in grasses to study dynamics wheat genome evolution (see publications).
The importance of diverse genetic input for success of crop breeding programs is well recognized. In contrast to ‘gene introgression’ involving transfer of one or a few genes from exotic and wild donors, ‘incorporation’ of a larger set of genes is better, particularly in context of productivity traits and would broaden the genetic base of wheat crop. We need to develop resources for efficient mining of wheat relatives which are highly diverse. The progenitor species like Aegilops tauschi Coss. the D genome donor of bread wheat and Triticum monococcum represents a rich source of resistance and productivity traits should be the first targets of mining. Meanwhile we need to develop genetic and genomic resources efficient mining of other wild relatives of wheat.
Mining the wheat gene pool. Taking forward my PhD project to identify and introgress traits of biotic, abiotic stress tolerance and productivity (see PhD publications) from Aegilops taushii into Bread wheat. We are characterizing the genetic diversity of Ae. tauschii to identify a core set of Ae tauschii which carries >90% of the genetic diversity of this species. On the other hand we are developing genomic resources (SNP markers) for assisting rapid and precise introgression from wild species (Ae. geniculate, Ae. speltoides, Ae. umbellulata, D. villosum, Th. intermedium, Th. elongatum, E. tsukushiensis, H. chilense and my other species) into cultivated wheat.
Identification and mapping of biotic and abiotic stress tolerance genes: Identified sources of leaf rust resistance and drought tolerance in wheat and developed several mapping populations for identification of genetic factors responsible for these agronomic traits. Mapped QTLs for drought and Karnal Bunt (see publications) and presently focusing on fine mapping of leaf rust gene Lr 42.
It is estimated that average annual yield increase of 2% will be needed for the estimated population increase, and this must be accomplished by increasing crop productivity per unit area of land. Wheat cropping systems also must contend with scenarios of limited water, fertilizer and the uncertainties of climate change. There is a universal agreement that we must unlock the biology of crop plants for sustainable and profitable crop production and increase the pace of crop improvement. Where DH and genomic selection increasing the breeding efficiency, hybrid wheat will aid in productivity and helps ensure a reliable, sustainable food supply.
Rapid advancement and yield potential. I was involved in Doubled haploid (DH) and hybrid wheat program during my doctoral studies (2001-2005). In DH program developed tiller culture protocol in wheat x maize crosses and developed thousands of DH lines. In HW program primarily made crosses for incorporating T. timopheevi cytoplasm to elite wheat lines. Restorer line breeding for T. timopheevi cytoplasm constitutes a major activity of program. Presently, working on nuclear male sterility and CMS system and transferring it to five elite winter and spring lines.
At present complex plants genome like wheat cannot be assembled using shotgun sequences from these short reads; however these sequences can be very useful in assembling the gene space(see pubications). Effort around the world are underway to use next generation sequencing to assemble gene space of diploid tetraploid and hexaploid bread wheat. These developments have stimulated interest in rapid characterization of agro-economic genes. Concurrently we have developed for next generation sequence and a TILLING population in diploid wheat.
Developing gene discovery model in diploid wheat. Sequencing and assembling T. monococcum subsp. aegilopoides (AmAm, ~30x, wild) and collaborating in sequencing of Tritcum monococcum subsp. monococcum (AmAm ,~150x, domesticated) (with CSHL). Developed large T. monococcum /T. aegilopoides RIL population (1,453 F6) and generating a high density GBS based SNP map to anchor Triticum monococcum genome map and also developed TILLING population (1700 M2’s) in same T. monococcum accession for gene discovery (see publications). These resources are being used for fine mapping of tillering gene (tin3) and gene discovery of other agronomic traits in T. monococcum.
Other physical maps: Aegilops tauschii is another diploid wheat and is progenitor of D genome of wheat with genome size over 4Gb. Involved in developing physical maps of Aegilops tauschii the progenitor species of wheat D genome (see publications) and chromosome 2A of wheat.
Sequencing of bread wheat genome: Participated in next generation sequencing of wheat genome and comparative sequence analysis with other grasses model genomes to study the evolution of wheat and identify gene space of wheat for faster crop improvement in wheat (see publications).
Ph.D.
Introgression of agro-economic traits from Aegilops taushii into Bread wheat. Characterized ~261 Ae. tauschii accessions for several (14) morphological /descriptor characters and evaluated for economic traits including resistance to Stripe rust, Leaf rust, Karnal bunt and cereal cyst nematodes to identify more than 10 accessions of Ae. taushii that could be donor for multiple traits.
Developed a protocol for rapid incorporation (direct cross) of economic traits from Ae. tauschii into bread wheat (see publications). This system led to recovery of a good number of F1s and BC1F1s thus, removing the major bottlenecks reported for direct cross system (Figure1). This system was employed to develop over 30 direct cross hybrids and back cross derivatives. Important high temperature tolerance improved like cell membrane stability and chlorophyll retention were transferred from Ae. tauschii to wheat Table 2 (see publications).
Figure1. A. Meiotic Metaphase-I showing 14 I + 7II in Aegilops tauschii x Triticum aestivum F1 hybrid (ABDD). B. Anaphase-I showing 56 chromosomes in colchicine treated Aegilops tauschii x Triticum aestivum F1 hybrid (AABBDDDD).
Developed 100 synthetic hexaploids (T. durum x Ae. tauschii) which can be used as a bridging stock for gene transfer to bread wheat for rust resistance.
Developed NIL populations (BC5F3 and BC5F4) for mapping and understanding the genetics of Karnal bunt (KB) resistance in the two NIL populations (see publications).