Ecology, Evolution and Organismal Biology

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Technological advances in maize breeding: past, present and future

2019-01-01 , Andorf, Carson , Beavis, William , Hufford, Matthew , Lubberstedt, Thomas , Smith, Stephen , Suza, Walter , Wang, Kan , Woodhouse, Margaret , Yu, Jianming , Lubberstedt, Thomas , Agronomy , Ecology, Evolution and Organismal Biology

Maize has for many decades been both one of the most important crops worldwide and one of the primary genetic model organisms. More recently, maize breeding has been impacted by rapid technological advances in sequencing and genotyping technology, transformation including genome editing, doubled haploid technology, parallelled by progress in data sciences and the development of novel breeding approaches utilizing genomic information. Herein, we report on past, current and future developments relevant for maize breeding with regard to (1) genome analysis, (2) germplasm diversity characterization and utilization, (3) manipulation of genetic diversity by transformation and genome editing, (4) inbred line development and hybrid seed production, (5) understanding and prediction of hybrid performance, (6) breeding methodology and (7) synthesis of opportunities and challenges for future maize breeding.

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Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data

2019-01-01 , Beiki, Hamid , Liu, Haibo , Huang, J. , Reecy, James , Manchanda, Nancy , Nonneman, D. , Smith, T. P. L. , Reecy, James , Tuggle, Christopher , Animal Science , Ecology, Evolution and Organismal Biology

Background: Our understanding of the pig transcriptome is limited. RNA transcript diversity among nine tissues was assessed using poly(A) selected single-molecule long-read isoform sequencing (Iso-seq) and Illumina RNA sequencing (RNA-seq) from a single White cross-bred pig.

Results: Across tissues, a total of 67,746 unique transcripts were observed, including 60.5% predicted proteincoding, 36.2% long non-coding RNA and 3.3% nonsense-mediated decay transcripts. On average, 90% of the splice junctions were supported by RNA-seq within tissue. A large proportion (80%) represented novel transcripts, mostly produced by known protein-coding genes (70%), while 17% corresponded to novel genes. On average, four transcripts per known gene (tpg) were identified; an increase over current EBI (1.9 tpg) and NCBI (2.9 tpg) annotations and closer to the number reported in human genome (4.2 tpg). Our new pig genome annotation extended more than 6000 known gene borders (5′ end extension, 3′ end extension, or both) compared to EBI or NCBI annotations. We validated a large proportion of these extensions by independent pig poly(A) selected 3′-RNAseq data, or human FANTOM5 Cap Analysis of Gene Expression data. Further, we detected 10,465 novel genes (81% non-coding) not reported in current pig genome annotations. More than 80% of these novel genes had transcripts detected in > 1 tissue. In addition, more than 80% of novel intergenic genes with at least one transcript detected in liver tissue had H3K4me3 or H3K36me3 peaks mapping to their promoter and gene body, respectively, in independent liver chromatin immunoprecipitation data.

Conclusions: These validated results show significant improvement over current pig genome annotations.

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A long-term N fertilizer gradient has little effect on soil organic matter in a high-intensity maize production system.

2014-02-01 , Castellano, Michael , Bach, Elizabeth , Drijber, Rhae , Hofmockel, Kirsten , Sawyer, John , Sawyer, John , Castellano, Michael , Agronomy , Ecology, Evolution and Organismal Biology

Global maize production alters an enormous soil organic C (SOC) stock, ultimately affecting greenhouse gas concentrations and the capacity of agroecosystems to buffer climate variability. Inorganic N fertilizer is perhaps the most important factor affecting SOC within maize-based systems due to its effects on crop residue production and SOC mineralization. Using a continuous maize cropping system with a 13 year N fertilizer gradient (0–269 kg N ha−1 yr−1) that created a large range in crop residue inputs (3.60–9.94 Mg dry matter ha−1 yr−1), we provide the first agronomic assessment of long-term N fertilizer effects on SOC with direct reference to N rates that are empirically determined to be insufficient, optimum, and excessive. Across the N fertilizer gradient, SOC in physico-chemically protected pools was not affected by N fertilizer rate or residue inputs. However, unprotected particulate organic matter (POM) fractions increased with residue inputs. Although N fertilizer was negatively linearly correlated with POM C/N ratios, the slope of this relationship decreased from the least decomposed POM pools (coarse POM) to the most decomposed POM pools (fine intra-aggregate POM). Moreover, C/N ratios of protected pools did not vary across N rates, suggesting little effect of N fertilizer on soil organic matter (SOM) after decomposition of POM. Comparing a N rate within 4% of agronomic optimum (208 kg N ha−1 yr−1) and an excessive N rate (269 kg N ha−1 yr−1), there were no differences between SOC amount, SOM C/N ratios, or microbial biomass and composition. These data suggest that excessive N fertilizer had little effect on SOM and they complement agronomic assessments of environmental N losses, that demonstrate N2O and NO3 emissions exponentially increase when agronomic optimum N is surpassed.

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Haplotype structure in commercial maize breeding programs in relation to key founder lines

2019-01-01 , Coffman, Stephanie , Hufford, Matthew , Andorf, Carson , Lubberstedt, Thomas , Lubberstedt, Thomas , Agronomy , Ecology, Evolution and Organismal Biology

Key message

High-density haplotype analysis revealed significant haplotype sharing between ex-PVPs registered from 1976 to 1992 and key maize founders, and uncovered similarities and differences in haplotype sharing patterns by company and heterotic group.


Proprietary inbreds developed by the private seed industry have been the major source for driving genetic gain in successful North American maize hybrids for decades. Much of the history of industry germplasm can be traced back to key founder lines, some of which were pivotal in the development of prominent heterotic groups. Previous studies have summarized pedigree-based relationships, genetic diversity and population structure among commercial inbreds with expired Plant Variety Protection (ex-PVP). However, less is known about the extent of haplotype sharing between historical founders and ex-PVPs. A better understanding of the relationships between founders and ex-PVPs provides insight into the haplotype and heterotic group structure among industry germplasm. We performed high-density haplotype analysis with 11.3 million SNPs on 212 maize inbreds, which included 157 ex-PVPs registered 1976–1992 and 55 public lines relevant to PVPs. Among these lines were 12 key founders identified in literature review: 207, A632, B14, B37, B73, LH123HT, LH82, Mo17, Oh43, OH7, PHG39 and Wf9. Our results revealed that, on average, 81.6% of an ex-PVP’s genome is shared with at least 1 of these 12 founder lines and more than half when limited to B73, Mo17 and 207. Quantifiable similarities and contrasts among heterotic groups and major US seed industry companies were also observed. The results from this study provide high-resolution haplotype data on ex-PVP germplasm, confirm founder relationship trends observed in previous studies, uncover region-specific haplotype structure differences and demonstrate how haplotype sharing analysis can be used as a tool to explore germplasm diversity.

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Bill size correlates with telomere length in male American Redstarts

2015-04-01 , Angelier, Frederic , Vleck, Carol , Vleck, Carol , Holberton, Rebecca , Marra, Peter , Ecology, Evolution and Organismal Biology

Telomere length (TL) has been shown to be a potential predictor of survival in wild vertebrates, and, as a consequence, there is growing interest in understanding the causes of inter-individual variability in TL. In that context, developmental conditions deserve a specific attention because they are thought to be a major driver of telomere shortening. Because poor developmental conditions can accelerate telomere shortening and impair growth (resulting in a small adult size), a positive correlation between TL and body size is expected. However, and surprisingly, the relationship between body size and telomere length has rarely been described in wild vertebrates. Here, we specifically examined this question in hatch-year (HY) and after hatch-year (AHY) male wintering American Redstarts (Setophaga ruticilla). Although tarsus size was not related to TL, we found a significant positive correlation between bill size and TL in HY male Redstarts, therefore supporting the idea that determinants of some components of individual size are also important determinants of TL in young birds. Moreover, this positive relationship between bill size and TL was also found for AHY birds, suggesting that adult TL may be, at least partly, explained by the telomere dynamics that occurred during the developmental phase.

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Identifying Miscanthus in Iowa

2015-10-01 , Boersma, Nic , Bonin, Catherine , Clark, Lynn , Heaton, Emily , Extension and Outreach , Agronomy , Ecology, Evolution and Organismal Biology

Do you know the difference between the Miscanthus species? One species of Miscanthus is now being evaluated for its bioenergy potential. However, two other species of Miscanthus are becoming invasive in the United States. Due to the invasive risk, this resource will help you learn to identify each species.

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Spatial Structuring of Cellulase Gene Abundance and Activity in Soil

2018-10-02 , Choi, Jinlyung , Bach, Elizabeth , Lee, Jaejin , Howe, Adina , Flater, Jared , Dooley, Shane , Howe, Adina , Hofmockel, Kirsten , Ecology, Evolution and Organismal Biology , Agricultural and Biosystems Engineering

Microbial mechanisms controlling cellulose degradation in soil habitats remains a critical knowledge gap in understanding and modeling terrestrial carbon-cycling. We investigated land management and soil micro-habitat influences on soil bacterial communities and distribution of cellulose-degrading enzyme genes in three bioenergy cropping systems (corn, prairie, and fertilized prairie). Within the soil, aggregates have been examined as potential micro- habitats with specific characteristics influencing resource partitioning and regulation, thus we also investigated genes associated with cellulose degradation within soil aggregate fractions from the fertilized prairie system. Soil bacterial communities and carbon-cycling gene presence varied across land management and soil microhabitats. Examination of genes specifically involved in cellulose-degradation pathways showed high levels of redundancy across the bioenergy cropping systems, but medium macroaggregates (1,000–2,000 μm) supported greater cellulose-degrading enzyme gene abundance than other aggregate fractions and whole soil. In medium aggregates, the enriched cellulose-degrading genes were most similar to genes previously observed in Actinobacteria. These findings represent gentic potential only, and our previous work on the same samples found elevated cellulase exo-enzyme activity in microaggregates. These contrasting results emphasize the importance of measuring community, functional genes, and metabolic potentials in a coordinated manner. Together, these data indicate that location within the soil matrix matters. Overall, our results indicate that soil aggregate environments are hot-spots that select for organisms with functional attributes like cellulose degradation, and future work should further explore micro-environmental factors that affect realized C-cycling processes.

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Telomere length, non-breeding habitat and return rate in male American redstarts

2013-01-01 , Angelier, Frederic , Vleck, Carol , Vleck, Carol , Holberton, Rebecca , Marra, Peter , Ecology, Evolution and Organismal Biology

  1. Telomeres are long repetitive noncoding sequences of DNA located at the ends of chromosomes. Recently, the study of telomere dynamics has been increasingly used to investigate ecological questions. However, little is currently known about the relationships that link environmental conditions, telomere dynamics and fitness in wild vertebrates.
  2. Using a small migratory bird (American redstart, Setophaga ruticilla), we investigated how telomere dynamics can be affected by non-breeding habitat quality and to what extent telomere length can predict the return rate of males.
  3. We show that telomeres shorten in most individuals over a 1-year period and, importantly, that telomeres of individuals wintering in a low-quality habitat shorten more than those of individuals wintering in a high-quality habitat.
  4. In addition, we found that longer telomeres are associated with a higher return rate than shorter telomeres, although the relationship between return rate and telomere length did not depend on habitat quality.
  5. Our study suggests that telomere dynamics are affected by environmental conditions and are related to indices of fitness in a migratory bird species.

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Trans-Gulf of Mexico loop migration of tree swallows revealed by solar geolocation

2014-01-01 , Bradley, David , Clark, Robert , Vleck, Carol , Dunn, Peter , Laughlin, Andrew , Taylor, Caz , Vleck, Carol , Whittingham, Linda , Winkler, David , Norris, D. Ryan , Ecology, Evolution and Organismal Biology

One of the greatest feats of avian migration is the non-stop crossing of extensive areas of inhospitable habitat such as deserts and seas. Differences in spring and autumn migration routes have been reported in species that cross such barriers, and are thought to have evolved in response to seasonal variation in prevailing wind direction. We tested the hypothesis that migration routes vary seasonally with respect to the Gulf of Mexico in the tree swallow Tachycineta bicolor using solar geolocators attached and retrieved at 4 breeding sites in central North America. We found that 100 % of birds (n = 10) made a trans-Gulf flight of >850 km from Louisiana south to their wintering grounds in the Yucatan Peninsula in 12–36 hours, achieving minimum ground speeds as high as 32 m/s. Although most days during autumn migration were characterized by unfavorable headwinds blowing to the northwest, migration over the Gulf mostly occurred on days with strong winds blowing to the south. In contrast, in 8 of 9 (88 %) birds on spring migration returned from the wintering grounds towards Louisiana following a clockwise loop pat tern flying over land to the west around the Gulf. During this spring period there were few days with prevailing winds from the south to assist northward migration. Results suggest that, despite being up to three times further (ca. 2,700 km), a coastal cir- cum-Gulf spring migration represents the less risky route when wind conditions are not favorable. These findings also help to re solve a long-standing dispute in the literature concerning migration patterns between the US Gulf coast and Mexico, and provide insight into the factors shaping migration strategies of small songbirds migrating across large bodies of water.

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Strategies to improve reference databases for soil microbiomes

2017-01-01 , Choi, Jinlyung , Howe, Adina , Yang, Fan , Stepanauskas, Ramunas , Cardenas, Erick , Garoutte, Aaron , Williams, Ryan , Flater, Jared , Tiedje, James , Hofmockel, Kirsten , Gelder, Brian , Howe, Adina , Ecology, Evolution and Organismal Biology , Agricultural and Biosystems Engineering