Biology subjects

Tuinstra, M. R.

Publications and source records attributed to Tuinstra, M. R..

4 recordsLinked to original sources

bioRxiv2021

A High-Resolution Method for the Systematic Detection of EMS-Induced Mutations in a Sequenced Population

The precise detection of causal DNA mutations is very crucial for forward genetic studies. Several sources of errors contribute to false-positive detections by current variant-calling algorithms, and these impact associating phenotypes with genotypes. To improve the accuracy of mutation detection we propose and implemented a high-resolution binning method for the accurate detection of likely EMS-induced mutations in a sequenced mutant population. The approach also incorporates a novel clustering algorithm for detecting likely false negatives with high accuracy. Sorghum bicolor is a very valuable crop species with tremendous potential for uncovering novel gene functions associated with highly desirable agronomical traits. We demonstrate the precision of the proposed method in the detection of likely EMS-induced mutations in the publicly available low-cost sequencing of the M3 generation from 600 sorghum BTx623 mutants. The method detected 3,274,606 single nucleotide polymorphisms (SNPs) of which 96% (3,141,908) were G/C to A/T DNA substitutions, as expected by EMS-mutagenesis action. We demonstrated the general applicability of the method, and showed a high concordance, 94% (3,074,759) SNPs overlap between SAMtools-based and GATK-based variant-calling algorithms. We also implemented a novel clustering algorithm which uncovered evidence for an additional 223,048 likely false-negative shared EMS-induced mutations. The final 3,497,654 SNPs represents an 87% increase in SNPs detected in the previous analysis of the sorghum mutant population. Annotation of the final SNPs revealed 10,263 high impact and 136,639 moderate impact SNPs, including 7,217 stop-gained mutations, and an average of 12 stop-gained mutations per mutant. We have implemented a public search database for this new genetic resource of 30,285 distinct sorghum genes containing medium or high impact EMS-induced mutations. Seedstock for a select 486 of the 600 described mutants are publicly available in the Germplasm Resources Information Network (GRIN) database.

bioinformatics↗

bioRxiv2019

Novel ankyrin-repeat mutant and modifiers of a kafirin mutant improve sorghum protein digestibility

Sorghum is a staple food for over 500 million people in Sub-Saharan Africa and Asia, however, sorghum proteins are poorly digested when wet-cooked. Three sorghum mutants were identified in a mutagenized population of the inbred line BTx623 that showed a 23-37% increase in wet-cooked protein digestibility compared to their unmutagenized parent. Furthermore, in comparison to the known high lysine, highly digestible sorghum mutant, P721Q, these mutants had 9% more protein overall that was 10% more digestible, had 12% more lysine, as well as better seed hardness. Using bulked segregant analysis based on whole genome sequencing data, we identified unique genomic regions on chromosome 5 of each EMS mutant that are associated with the increase in protein digestibility. Analyzing shared mutations in candidate genes, the high protein digestibility phenotype in one mutant is linked to a point mutation in a novel, ankyrin repeat protein. In another, the increase is associated with a mutation in a kafirin gene and suggests novel genetic modifiers. This study provides material and molecular markers that can be used to enhance sorghum nutritional value, contribute to fighting malnutrition and elucidate new roles for ankyrin-repeat proteins in plants. One sentence summaryMutations in a novel, ankyrin domain protein and genetic modifiers of a known mutation in a seed storage protein lead to increased digestibility of seed proteins in sorghum after wet cooking.

plant biology↗

bioRxiv2019

The relevance of dominance and functional annotations to predict agronomic traits in hybrid maize

Heterosis has been key to the development of maize breeding but describing its genetic basis has been challenging. Previous studies of heterosis have shown the contribution of within-locus complementation effects (dominance) and their differential importance across genomic regions. However, they have generally considered panels of limited genetic diversity and have shown little benefit to including dominance effects for predicting genotypic value in breeding populations. This study examined within-locus complementation and enrichment of genetic effects by functional classes in maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the United States (1,106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1,640 hybrids). We assayed three agronomic traits: days to silking (DTS), plant height (PH) and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results point to mechanisms by which heterosis arises through local complementation in proximal gene regions and suggest the relevance of dominance and gene annotations for genomic prediction in maize.

genomics↗

bioRxiv2017

Genetic Analysis of Lodging in Diverse Maize Hybrids

Damage caused by lodging is a significant problem in corn production that results in estimated annual yield losses of 5-20%. Over the past 100 years, substantial maize breeding efforts have increased lodging resistance by artificial selection. However, less research has focused on understanding the genetic architecture underlying lodging. Lodging is a problematic trait to evaluate since it is greatly influenced by environmental factors such as wind, rain, and insect infestation, which make replication difficult. In this study over 1,723 diverse inbred maize genotypes were crossed to a common tester and evaluated in five environments over multiple years. Natural lodging due to severe weather conditions occurred in all five environments. By testing a large population of genetically diverse maize lines in multiple field environments, we detected significant correlations for this highly environmentally influenced trait across environments and with important agronomic traits such as yield and plant height. This study also permitted the mapping of quantitative trait loci (QTL) for lodging. Several QTL identified in this study overlapped with loci previously mapped for stalk strength in related maize inbred lines. QTL intervals mapped in this study also overlapped candidate genes implicated in the regulation of lignin and cellulose synthesis.

genetics↗