Minimum stomatal conductance: implications for describing the genetic control of transpiration

2013 Fall.Includes bibliographical references.Minimum stomatal conductance (g0) makes a significant contribution to the rate of water loss in plants. The influence of g0 on water use efficiency (WUE) has implications for plant drought tolerance and adaptation, thus we propose that g0 can be used as a trait to describe the genetic control of water use in leaf transpiration models. In the model species, Arabidopsis thaliana, g0 exhibits both environmental and genetic variation. We explored one g0 quantitative trait locus (QTL) by measuring and simulating transpiration for two A. thaliana accessions Kas-1 and Tsu-1, as well as recombinant inbred lines (RILs) from a reciprocal cross of the two parental lines. Using a three-dimensional spatially explicit plant process model, MAESTRA, we aimed to: (1) test the accuracy of transpiration prediction for Kas-1 and Tsu-1 using measured g0 values, (2) parameterize MAESTRA with Tsu-1, Kas-1, and RIL g0 values to predict transpiration of RILs containing either Tsu-1 and Kas-1 alleles at the g0 QTL, and (3) determine if a relationship exists between g0 values under well-watered and drought conditions in A. thaliana. MAESTRA accurately predicted A. thaliana transpiration for Kas-1 and Tsu-1 accessions when parameterized with measured g0 values. There was no significant difference between measured and simulated transpiration estimates for both accessions, with Tsu-1 simulated transpiration 5.2% lower than the mean measured, and Kas-1 simulated transpiration 1.4% higher than measured. On average, Kas-1 transpired 73% as much water as Tsu-1. Due to the lack of specific knowledge of RIL physiology aside from g0, simulating RIL transpiration with varying g0 values yielded non-significant results. However, based on the simulated means for RIL transpiration using RIL, Kas-1, and Tsu-1 g0 values, we show that g0 parameterization predicts daily transpiration when all other parameters are held constant at Tsu-1 or Kas-1 measured and presumed physiology. This further points to the importance of g0 for transpiration predictions. Data on additional g0 QTL could aid in predicting transpiration from novel genotypes such as RILs containing multiple combinations of alleles from parental genotypes. We found that accessions with relatively high well-watered g0 values showed sharper declines in g0 during drought compared to accessions with lower g0 values under well-watered conditions (p < 0.0001). The use of plant physiological models for predicting transpiration of novel genetic lines will benefit from the further knowledge of the genetic control of g0

Development of a Next-Generation NIL Library in Arabidopsis Thaliana for Dissecting Complex Traits

The identification of the loci and specific alleles underlying variation in quantitative traits is an important goal for evolutionary biologists and breeders. Despite major advancements in genomics technology, moving from QTL to causal alleles remains a major challenge in genetics research. Near-isogenic lines are the ideal raw material for QTL validation, refinement of QTL location and, ultimately, gene discovery. Results: In this study, a population of 75 Arabidopsis thaliana near-isogenic lines was developed from an existing recombinant inbred line (RIL) population derived from a cross between physiologically divergent accessions Kas-1 and Tsu-1. First, a novel algorithm was developed to utilize genome-wide marker data in selecting RILs fully isogenic to Kas-1 for a single chromosome. Seven such RILs were used in 2 generations of crossing to Tsu-1 to create BC1 seed. BC1 plants were genotyped with SSR markers so that lines could be selected that carried Kas-1 introgressions, resulting in a population carrying chromosomal introgressions spanning the genome. BC1 lines were genotyped with 48 genome-wide SSRs to identify lines with a targeted Kas-1 introgression and the fewest genomic introgressions elsewhere. 75 such lines were selected and genotyped at an additional 41 SNP loci and another 930 tags using 2b-RAD genotyping by sequencing. The final population carried an average of 1.35 homozygous and 2.49 heterozygous introgressions per line with average introgression sizes of 5.32 and 5.16 Mb, respectively. In a simple case study, we demonstrate the advantage of maintaining heterozygotes in our library whereby fine-mapping efforts are conducted simply by self-pollination. Crossovers in the heterozygous interval during this single selfing generation break the introgression into smaller, homozygous fragments (sub-NILs). Additionally, we utilize a homozygous NIL for validation of a QTL underlying stomatal conductance, a low heritability trait. Conclusions: The present results introduce a new and valuable resource to the Brassicaceae research community that enables rapid fine-mapping of candidate loci in parallel with QTL validation. These attributes along with dense marker coverage and genome-wide chromosomal introgressions make this population an ideal starting point for discovery of genes underlying important complex traits of agricultural and ecological significance.NSF DEB-1022196, DEB-0618302, DEB-0618347, IOS-09221457Integrative Biolog

Development of a next-generation NIL library in Arabidopsis thaliana for dissecting complex traits

Background: The identification of the loci and specific alleles underlying variation in quantitative traits is an important goal for evolutionary biologists and breeders. Despite major advancements in genomics technology, moving from QTL to causal alleles remains a major challenge in genetics research. Near-isogenic lines are the ideal raw material for QTL validation, refinement of QTL location and, ultimately, gene discovery. Results: In this study, a population of 75 Arabidopsis thaliana near-isogenic lines was developed from an existing recombinant inbred line (RIL) population derived from a cross between physiologically divergent accessions Kas-1 and Tsu-1. First, a novel algorithm was developed to utilize genome-wide marker data in selecting RILs fully isogenic to Kas-1 for a single chromosome. Seven such RILs were used in 2 generations of crossing to Tsu-1 to create BC1 seed. BC1 plants were genotyped with SSR markers so that lines could be selected that carried Kas-1 introgressions, resulting in a population carrying chromosomal introgressions spanning the genome. BC1 lines were genotyped with 48 genome-wide SSRs to identify lines with a targeted Kas-1 introgression and the fewest genomic introgressions elsewhere. 75 such lines were selected and genotyped at an additional 41 SNP loci and another 930 tags using 2b-RAD genotyping by sequencing. The final population carried an average of 1.35 homozygous and 2.49 heterozygous introgressions per line with average introgression sizes of 5.32 and 5.16 Mb, respectively. In a simple case study, we demonstrate the advantage of maintaining heterozygotes in our library whereby fine-mapping efforts are conducted simply by self-pollination. Crossovers in the heterozygous interval during this single selfing generation break the introgression into smaller, homozygous fragments (sub-NILs). Additionally, we utilize a homozygous NIL for validation of a QTL underlying stomatal conductance, a low heritability trait. Conclusions: The present results introduce a new and valuable resource to the Brassicaceae research community that enables rapid fine-mapping of candidate loci in parallel with QTL validation. These attributes along with dense marker coverage and genome-wide chromosomal introgressions make this population an ideal starting point for discovery of genes underlying important complex traits of agricultural and ecological significance.Keywords: Stomatal conductance, Quantitative trait loci, 2b-RAD, Fine-mappingKeywords: Stomatal conductance, Quantitative trait loci, 2b-RAD, Fine-mappin