Biology subjects

Haas, M. W.

Publications and source records attributed to Haas, M. W..

4 recordsLinked to original sources

bioRxiv2026

Transcriptional architecture underlying development, adaptation, and domestication in Northern Wild Rice (Zizania palustris L.)

AO_SCPLOWBSTRACTC_SCPLOWZizania palustris (Northern Wild Rice) is an aquatic grass native to North America and a crop wild relative of Oryza sativa with ecological, cultural, and agricultural significance. Here, we present a transcriptomic atlas spanning 20 tissues across six major developmental stages. Seed tissues showed shifts in abscisic acid, gibberellin, and ethylene pathways that define the hormonal basis of deep dormancy in this recalcitrant species and its release. Leaf development showed stage-specific reprogramming, from hypoxia-responsive programs in submerged tissues to cell wall remodeling and redox regulation during aquatic-aerial transitions, with photosynthesis and carbohydrate metabolism defining flag leaves and SRG1 divergence emerging as a defining feature of leaf development in Z. palustris. Reproductive tissues expressed duplicated homologs of well-recognized shattering genes with divergent regulation, consistent with subfunctionalization after whole-genome duplication. These findings provide new insight into traits underlying ecological adaptation and domestication in Z. palustris and related grasses. CORE IDEASO_LIA first transcriptomic atlas for Northern Wild Rice maps gene expression across 20 tissues and six developmental stages, providing a foundational functional genomics resource for Zizania palustris. C_LIO_LISeed dormancy and release are driven by coordinated hormone reprogramming, with shifts in ABA, GA, and ethylene pathways across whole seed, embryo, and endosperm. C_LIO_LILeaf development is defined by aquatic-to-aerial transcriptional transitions, moving from hypoxia-responsive programs in submerged tissues to cell wall remodeling, redox regulation, and photosynthesis/metabolism in aerial and flag leaves. C_LIO_LIWhole-genome duplication underlies regulatory divergence in domestication traits, as duplicated homologs of canonical seed shattering genes show paralog- and tissue-specific expression consistent with subfunctionalization. C_LIO_LIThe atlas identifies tissue-specific modules and stable housekeeping candidates, enabling improved experimental design (e.g., expression normalization) and accelerating candidate prioritization for breeding, GWAS/eQTL, and trait discovery. C_LI PLAIN LANGUAGE SUMMARYNorthern Wild Rice (Zizania palustris) is an aquatic grass native to North America that is important for ecosystems, agriculture, and Indigenous cultures. In this study, we created a detailed gene expression map across 20 different tissues and six stages of plant development. We found that seeds strongly regulate plant hormones that control dormancy, helping explain why Northern Wild Rice seeds remain dormant for long periods and how they eventually germinate. Leaves showed clear changes in gene activity as plants moved from underwater growth to above-water growth, shifting from low-oxygen stress responses to processes that support photosynthesis and structural strength. In flowers, we identified duplicated genes involved in seed shattering that are regulated differently, likely due to past genome duplication events. Together, these results improve our understanding of how Northern Wild Rice is adapted to aquatic environments and how key traits relevant to domestication have evolved.

plant biology↗

bioRxiv2022

Genetic Analysis of Wild and Cultivated Populations of Northern Wild Rice (Zizania palustris L.) Reveal New Insights into Gene Flow and Domestication

Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic, annual grass with significant ecological, cultural, and economic importance to the Great Lakes region of North America. In this study, we assembled and genotyped a diverse collection of 839 NWR individuals using genotyping-by-sequencing (GBS) and obtained 5,955 single-nucleotide polymorphisms (SNPs). Our collection consisted of samples from 12 wild NWR populations collected across Minnesota and Western Wisconsin, some of which were collected over two time points; a representative collection of cultivated NWR varieties and breeding populations; and a Zizania aquatica outgroup. Using these data, we characterized the genetic diversity, relatedness, and population structure of this broad collection of NWR genotypes. We found that wild populations of NWR clustered primarily by their geographical location, with some clustering patterns likely influenced by historical ecosystem management. Cultivated populations were genetically distinct from wild populations, suggesting limited gene flow between the semi-domesticated crop and its wild counterparts. The first genome-wide scans of putative selection events in cultivated NWR suggest that the crop is undergoing heavy selection pressure for traits conducive to irrigated paddy conditions. Overall, this study presents a large set of SNP markers for use in NWR genetic studies and provides new insights into the gene flow, history, and complexity of wild and cultivated populations of NWR.

genetics↗

bioRxiv2021

Whole Genome Assembly and Annotation of Northern Wild Rice, Zizania palustris L., Supports a Whole Genome Duplication in the Zizania Genus

Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic grass native to North America that is notable for its nutritious grain. This is an important species with ecological, cultural, and agricultural significance, specifically in the Great Lakes region of the United States. Using long- and short-range sequencing, Hi-C scaffolding, and RNA-seq data from eight tissues, we generated an annotated whole genome de novo assembly of NWR. The assembly is 1.29 Gb, highly repetitive ([~]76.0%), and contains 46,421 putative protein-coding genes. The expansion of retrotransposons within the genome and a whole genome duplication prior to the Zizania-Oryza speciation event have both led to an increase in genome size of NWR in comparison with O. sativa and Z. latifolia. Both events depict a genome rapidly undergoing change over a short evolutionary time. Comparative analyses revealed conservation of large syntenic blocks with Oryza sativa L., which were used to identify putative seed shattering genes. Estimates of divergence times revealed the Zizania genus diverged from Oryza [~]26-30 million years ago (MYA), while NWR and Zizania latifolia diverged from one another [~]6-8 MYA. Comparative genomics confirmed evidence of a whole genome duplication in the Zizania genus and provided support that the event was prior to the NWR-Z. latifolia speciation event. This high-quality genome assembly and annotation provides a valuable resource for comparative genomics in the Oryzeae tribe and provides an important resource for future conservation and breeding efforts of NWR.

genomics↗

bioRxiv2019

Linear modeling reveals a predominance of cis- over trans- regulatory effects in wild and domesticated barley

Barley, like other crops, has experienced a series of genetic changes that have impacted its architecture and growth habit to suit the needs of humans, termed the domestication syndrome. Domestication also resulted in a concomitant bottleneck that reduced sequence diversity in genes and regulatory regions. Little is known about regulatory changes resulting from domestication in barley. We used RNA-seq to examine allele-specific expression (ASE) in hybrids between wild and domesticated barley. Our results show that most genes have conserved regulation. In contrast to studies of allele specific expression in interspecific hybrids, we find almost a complete absence of trans effects. We also find that cis regulation is largely stable in response to short-term cold stress. Our study has practical implications for crop improvement using wild relatives. Genes regulated in cis are more likely to be expressed in a new genetic background at the same level as in their native background.

genetics↗