Engineering topics

Kaeppler, Shawn M.

Publications and source records attributed to Kaeppler, Shawn M..

6 records

DOE OSTI2023

Transcription factor bHLH121 regulates root cortical aerenchyma formation in maize

Root anatomical phenotypes present a promising yet underexploited avenue to deliver major improvements in yield and climate resilience of crops by improving water and nutrient uptake. For instance, the formation of root cortical aerenchyma (RCA) significantly increases soil exploration and resource capture by reducing the metabolic costs of root tissue. A key bottleneck in studying such phenotypes has been the lack of robust high-throughput anatomical phenotyping platforms. We exploited a phenotyping approach based on laser ablation tomography, termed Anatomics , to quantify variation in RCA formation of 436 diverse maize lines in the field. Results revealed a significant and heritable variation for RCA formation. Genome-wide association studies identified a single-nucleotide polymorphism mapping to a root cortex-expressed gene-encoding transcription factor bHLH121. Functional studies identified that the bHLH121 Mu transposon mutant line and CRISPR/Cas9 loss-of-function mutant line showed reduced RCA formation, whereas an overexpression line exhibited significantly greater RCA formation when compared to the wild-type line. Characterization of these lines under suboptimal water and nitrogen availability in multiple soil environments revealed that bHLH121 is required for RCA formation developmentally as well as under studied abiotic stress. Overall functional validation of the bHLH121 gene’s importance in RCA formation provides a functional marker to select varieties with improved soil exploration and thus yield under suboptimal conditions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Utility of anthesis–silking interval information to predict grain yield under water and nitrogen limited conditions

Delayed silking relative to pollen shed, measured as the anthesis–silking interval (ASI, the period between pollen shed and silking), is a good indicator of response to abiotic stresses in maize ( Zea mays L.). This research was conducted to investigate how ASI is affected by nitrogen (N) and water availability and to assess the utility of ASI to indirectly predict grain yield (GY) under contrasting water and N treatments. Two experiments were conducted in Hancock, WI, in 2018 and 2019. One experiment (Diverse hybrids) included 302 hybrids resulting from the cross of diverse inbred lines by a single tester evaluated at four different treatment levels resulting from combining nonlimited and low N with nonlimited and low water treatments. The second experiment (NSS FAC) included a set of 408 hybrids derived from the cross of biparental doubled-haploid lines from 13 factorial populations and evaluated under nonlimited and low N treatments. Anthesis and silk time in growing degree days, and GY (Mg ha -1 ) were measured. Genomic prediction was assessed using a genomic best linear unbiased prediction model, and predictive ability was calculated as the correlation between genomic predictions and adjusted means in the different treatments. Predictive ability ranged from .15 to .49 for NSS FAC and from .06 to .51 for Diverse hybrids across traits and treatments. The ASI was a good indicator of stress and showed higher heritability than GY in the limited treatments for both experiments; however, it did not improve yield predictability.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Strong parallel evidence of selection during switchgrass sward establishment in hybrid and lowland ecotypes

Switchgrass sward establishment results in up to 90% seedling mortality. The degree of selection during sward establishment has not been reported using modern genetic methods. Pooled leaf samples were sequenced from replicated swards of 46 half-sib families from two breeding groups (lowland and hybrid) before and through 3 years of stand establishment. Pooled allele frequencies were then assessed using fixation indices (Fst) and an independent data set was used to predict the polygenic impact of establishment selection on two traits (heading date and winter survivorship). Last, the DNA pools were assigned survival rankings to predict the sward survival genomically estimated breeding values within the training data set. Strong and parallel selection occured in both breeding groups. Five genomic regions exceeded the significant threshold of 99.9% in >10 families, indicating consistent selection across families and breeding groups. Polygenic trait predictions determined that establishment selection was partially associated with winter survivorship but resulted in variable heading date alterations. The genomewide variation is consistent with selection for a small number of related parental lines. This study observed strong selection for a small number of hybrid and coastal ecotype individuals which are promising germplasm sources for improved sward survival. This confirms prior reports of sward selection during grassland establishment and highlights the strength of pooled DNA sequencing for survival traits.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Genomic variation within the maize stiff-stalk heterotic germplasm pool

The stiff-stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four expired Plant Variety Protection (ex-PVP) lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40, which is a Pioneer Hi-Bred International (PHI) early stiff-stalk type. Sequence was generated using long-read sequencing achieving highly contiguous assemblies of 2.13-2.18 Gbp with N50 scaffold lengths >200 Mbp. Inbred-specific gene annotations were generated using a core five-tissue gene expression atlas, whereas transposable element (TE) annotation was conducted using de novo and homology-directed methodologies. Compared with the reference inbred B73, synteny analyses revealed extensive collinearity across the five stiff-stalk genomes, although unique components of the maize pangenome were detected. Comparison of this set of stiff-stalk inbreds with the original Iowa Stiff Stalk Synthetic breeding population revealed that these inbreds represent only a proportion of variation in the original stiff-stalk pool and there are highly conserved haplotypes in released public and ex-Plant Variety Protection inbreds. Despite the reduction in variation from the original stiff-stalk population, substantial genetic and genomic variation was identified supporting the potential for continued breeding success in this pool. The assemblies described here represent stiff-stalk inbreds that have historical and commercial relevance and provide further insight into the emerging maize pangenome.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Root angle in maize influences nitrogen capture and is regulated by calcineurin B-like protein (CBL)-interacting serine/threonine-protein kinase 15 ( ZmCIPK15 )

Crops with reduced nutrient and water requirements are urgently needed in global agriculture. Root growth angle plays an important role in nutrient and water acquisition. A maize diversity panel of 481 genotypes was screened for variation in root angle employing a high-throughput field phenotyping platform. Genome-wide association mapping identified several single nucleotide polymorphisms (SNPs) associated with root angle, including one located in the root expressed CBL-interacting serine/threonine-protein kinase 15 (ZmCIPK15) gene (LOC100285495). Reverse genetic studies validated the functional importance of ZmCIPK15, causing a approximately 10° change in root angle in specific nodal positions. A steeper root growth angle improved nitrogen capture in silico and in the field. OpenSimRoot simulations predicted at 40 days of growth that this change in angle would improve nitrogen uptake by 11% and plant biomass by 4% in low nitrogen conditions. In field studies under suboptimal N availability, the cipk15 mutant with steeper growth angles had 18% greater shoot biomass and 29% greater shoot nitrogen accumulation compared to the wild type after 70 days of growth. We propose that a steeper root growth angle modulated by ZmCIPK15 will facilitate efforts to develop new crop varieties with optimal root architecture for improved performance under edaphic stress.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Single‐parent expression drives dynamic gene expression complementation in maize hybrids

SUMMARY Single‐parent expression (SPE) is defined as gene expression in only one of the two parents. SPE can arise from differential expression between parental alleles, termed non‐presence/absence (non‐PAV) SPE, or from the physical absence of a gene in one parent, termed PAV SPE. We used transcriptome data of diverse Zea mays (maize) inbreds and hybrids, including 401 samples from five different tissues, to test for differences between these types of SPE genes. Although commonly observed, SPE is highly genotype and tissue specific. A positive correlation was observed between the genetic distance of the two inbred parents and the number of SPE genes identified. Regulatory analysis showed that PAV SPE and non‐PAV SPE genes are mainly regulated by cis effects, with a small fraction under trans regulation. Polymorphic transposable element insertions in promoter sequences contributed to the high level of cis regulation for PAV SPE and non‐PAV SPE genes. PAV SPE genes were more frequently expressed in hybrids than non‐PAV SPE genes. The expression of parentally silent alleles in hybrids of non‐PAV SPE genes was relatively rare but occurred in most hybrids. Non‐PAV SPE genes with expression of the silent allele in hybrids are more likely to exhibit above high parent expression level than hybrids that do not express the silent allele, leading to non‐additive expression. This study provides a comprehensive understanding of the nature of non‐PAV SPE and PAV SPE genes and their roles in gene expression complementation in maize hybrids.

Li, Zhi↗