A toolkit to rapidly modify root systems through single plant selection

Background The incorporation of root traits into elite germplasm is typically a slow process. Thus, innovative approaches are required to accelerate research and pre-breeding programs targeting root traits to improve yield stability in different environments and soil types. Marker-assisted selection (MAS) can help to speed up the process by selecting key genes or quantitative trait loci (QTL) associated with root traits. However, this approach is limited due to the complex genetic control of root traits and the limited number of well-characterised large effect QTL. Coupling MAS with phenotyping could increase the reliability of selection. Here we present a useful framework to rapidly modify root traits in elite germplasm. In this wheat exemplar, a single plant selection (SPS) approach combined three main elements: phenotypic selection (in this case for seminal root angle); MAS using KASP markers (targeting a root biomass QTL); and speed breeding to accelerate each cycle. Results To develop a SPS approach that integrates non-destructive screening for seminal root angle and root biomass, two initial experiments were conducted. Firstly, we demonstrated that transplanting wheat seedlings from clear pots (for seminal root angle assessment) into sand pots (for root biomass assessment) did not impact the ability to differentiate genotypes with high and low root biomass. Secondly, we demonstrated that visual scores for root biomass were correlated with root dry weight (r = 0.72), indicating that single plants could be evaluated for root biomass in a non-destructive manner. To highlight the potential of the approach, we applied SPS in a backcrossing program which integrated MAS and speed breeding for the purpose of rapidly modifying the root system of elite bread wheat line Borlaug100. Bi-directional selection for root angle in segregating generations successfully shifted the mean root angle by 30° in the subsequent generation (P ≤ 0.05). Within 18 months, BC2F4:F5 introgression lines were developed that displayed a full range of root configurations, while retaining similar above-ground traits to the recurrent parent. Notably, the seminal root angle displayed by introgression lines varied more than 30° compared to the recurrent parent, resulting in lines with both narrow and wide root angles, and high and low root biomass phenotypes. Conclusion The SPS approach enables researchers and plant breeders to rapidly manipulate root traits of future crop varieties, which could help improve productivity in the face of increasing environmental fluctuations. The newly developed elite wheat lines with modified root traits provide valuable materials to study the value of different root systems to support yield in different environments and soil types.

Root Trait Diversity in Field Grown Durum Wheat and Comparison with Seedlings

Roots are important for crop adaptation, particularly in dryland environments. We evaluated root development of 37 durum wheat genotypes (modern cultivars and landraces) in the field at the adult plant stage, through a shovelomics approach. Large genotypic variability was found for root traits. Differences between the landraces and modern cultivars were the main driver of this variation, with landraces showing higher plant vigor for roots and shoots. Nonetheless, genotypic variation within groups was also observed, related to different models of root growth, largely independent of total root length. These two models represented root growth were oriented either to occupy more soil volume, or to occupy less soil volume with increased density. The field results were then compared with root data previously collected in seedlings using a filter paper-based method, to assess whether early root anticipated adult root features. Field plants showed a narrower root angle than seedlings. In particular, landraces presented a narrower root angle than cultivars, but only at seedling stage. Potentially useful correlations were found between the two growth stages for root length and number.

Modified median hepatic fissure approach for resection of liver tumours located in the angle between the root of the middle and right hepatic veins

Background Liver tumours between the root angle of the middle and right hepatic veins are a special type of liver segment VIII tumour. In this study, we designed a modified median hepatic fissure approach to remove these tumours. The safety and effectiveness of the approach were evaluated. Materials and methods From April 2015 to November 2019, 11 patients with liver tumours between the angle of the middle and right hepatic veins underwent this modified median hepatic fissure approach. We retrospectively analysed data from the perioperative periods of these 11 patients, including general condition, operation time, intraoperative bleeding, and postoperative complications. Disease-free survival and overall survival were assessed. Results Of the 11 patients, 9 patients had primary hepatocellular carcinoma and 2 had colorectal liver metastases. The average intraoperative blood loss was 285 mL (150–450 mL). Two patients developed postoperative bile leakage, but there were no significant serious complications, such as intraabdominal bleeding and liver failure, in any of the patients. The liver function returned to the normal range on the 5th day after surgery. Of the 11 patients, 5 have survived for more than 3 years (45.5%), and 4 have been disease-free for more than 3 years (36.3%). Conclusions For liver tumours between the root angle of the middle and right hepatic veins, the modified median hepatic fissure approach is a safe and feasible method.

Variation in Root System Architecture among the Founder Parents of Two 8-way MAGIC Wheat Populations for Selection in Breeding

Root system architecture (RSA) is a target for breeding crops with effective nutrient and water use. Breeding can use populations designed to map quantitative trait loci (QTL). Here we non-invasively phenotype roots and leaves of the 16 foundation parents of two multi-parent advanced generation inter-cross (MAGIC) populations, covering diversity in spring (CSIRO MAGIC) and winter (NIAB MAGIC) wheats. RSA components varied after 16 days in the upgraded, paper-based imaging platform, GrowScreen-PaGe: lateral root length 2.2 fold; total root length, 1.9 fold; and seminal root angle 1.2 fold. RSA components total and lateral root length had the highest root heritabilities (H2) (H2 = 0.4 for CSIRO and NIAB parents) and good repeatability (r = 0.7) in the GrowScreen-PaGe. These can be combined with leaf length (H2 = 0.8 CSIRO; 0.7 NIAB) and number (H2 = 0.6 CSIRO; 0.7 NIAB) to identify root and shoot QTL to breed for wheats with vigorous RSA and shoot growth at establishment, a critical phase for crop productivity. Time resolved phenotyping of MAGIC wheats also revealed parents to cross in future for growth rate traits (fastest: Robigus–NIAB and AC Barrie–CSIRO; slowest Rialto–NIAB and G204 Xiaoyan54–CSIRO) and root: shoot allocation traits (fast growers grew roots, notably laterals, quicker than leaves, compared to slow growers).

Adaptation To Soil Acidity By Common Beans (Phaseolus Vulgaris L.) is Associated With Root Morphological Traits and Structures

Aims Common bean is an important source of food and fodder and is used to improve soil fertility when integrated in cropping systems through intercropping or rotation. Although widely grown by smallholders in Ethiopia, its productivity is constrained by several factors including soil acidity, which limits nutrient availability and uptake. The negative effects of soil acidity may be mediated by root system morphology and structure. Therefore, the aim of this study was to determine if root traits in common bean are associated with tolerance to soil acidity. Methodology The study was laid out in a split-plot design, whereby soil amendment practices with phosphorus (+P or -P) and liming (+lime or –lime) and their combinations were assigned to main plots and varieties to subplots. Two improved varieties (Nasir and Deme) and two farmers’ varieties (Polpole and Pantarkin) of common bean were evaluated under each soil amendment practice. Results Farmers’ variety Polpole produced significantly (p< 0.05) more hypocotyl roots (14.17) with a wider hypocotyls angle (5.87°) than other varieties. In addition, Polpole had a larger tap root diameter (2.57 mm) and length (34.10 cm) in plots amended with P. The improved variety Deme showed a higher number of basal roots (14.0) and basal root whorls (4.20) as well as lower basal root angle (0-15°) in plots amended with P and lime. Analyses demonstrate that common bean varieties differ in their ability to tolerate soil acidity due to differences in their root morphological and structural traits. Conclusion The results suggest an opportunity to identify and further develop acid tolerant varieties for low input farming systems to improve and enhance bean productivity and efficiency of the agro ecosystem at large.

Genome-Wide Association Study (GWAS) Reveals The Genetic Basis of Brace Root Angle and Diameter in Maize

Background:Brace roots are an important part of the maize root system. Among brace root traits, brace root angle (BRA) and brace root diameter (BRD) are important components that affect plant growth and development. However, there are no reports on the genetic basis of maize BRA and BRD. Results:Here, a genome-wide association study (GWAS) was conducted using 508 associated populations with extensive natural variation. The broad heritability of BRA and BRD reached 0.91 and 0.82, respectively. The analysis of different subgroups showed that there were significant differences in BRA traits in different subgroups, whereas there was no significant difference in BRD. Evaluation of phenotypic diversity in three different environments showed that BRA and BRD exhibit a wide range of natural variability. In the GWAS, the BRA and BRD were combined with 55,8629 single nucleotide polymorphisms, and four candidate genes were found for BRA within the threshold of P < 1.78×10-6 that were significantly related to BRD). These genes may (1) participate in maize brace root cell wall synthesis through cell transport (GRMZM2G479243); (2) involve hormone signaling pathways in the horizontal expansion of brace root cells (GRMZM2G101928 and GRMZM2G174736); or (3) involve the PLETHORA (PLT1/2) gene (GRMZM2G151934) to promote stem cells and transport expanded cells to affect the growth of root meristems.Conclusions:These results provide theoretical information for understanding the genetic basis of brace root development. Further research on candidate genes will help clarify the molecular pathways regulating BRA and BRD in maize.

Analysis of the sagittal root angle and its correlation with hard and soft tissue indices in anterior teeth for immediate implant evaluation: a retrospective study

Background To assess the root angle characteristics of maxillary incisors, and to analyze the relationship between the root angle and other implant-related anatomical indices to use the sagittal root angle as an index for immediate implant evaluation and design. Methods A random sample consisting of 400 cone-beam computed tomography (CBCT) images and 65 maxillary plaster models were selected for the present study. CBCT and stereolithography (STL) scan images were imported as DICOM files into coDiagnostiX software for matching the hard and soft tissue. The angle between the long axis of the anterior tooth and the corresponding alveolar bone and implant-related hard and soft tissue indices were measured in the sagittal section. Descriptive statistics, frequency analysis, multi-level comparisons, and correlation analyses were performed. Results The average sagittal root angles were 15° at the central incisor and 19° at the lateral incisor. The root angle in males was significantly larger than that in females, and increased with age. The largest angle, 22.35°, was found in the lateral incisors of the oldest (> 50 years old) male group. The root angle was found to correlate with coronal buccal bone thickness, coronal palatal bone thickness, apical buccal bone thickness, palatal bone thickness, and the below apex bone thickness. Conclusions The sagittal root angle could reflect the distribution of other implant-related anatomical indices, which may provide additional reference for the evaluation of immediate implant placement.

Associated SNPs, Heritabilities, Trait Correlations, and Genomic Breeding Values for Resistance in Snap Beans (Phaseolus vulgaris L.) to Root Rot Caused by Fusarium solani (Mart.) f. sp. phaseoli (Burkholder)

Root rot is a major constraint to snap bean (Phaseolus vulgaris) production in the United States and around the world. Genetic resistance is needed to effectively control root rot disease because cultural control methods are ineffective, and the pathogen will be present at the end of one season of production on previously clean land. A diversity panel of 149 snap bean pure lines was evaluated for resistance to Fusarium root rot in Oregon. Morphological traits potentially associated with root rot resistance, such as aboveground biomass, adventitious roots, taproot diameter, basal root diameter, deepest root angle, shallowest root angle, root angle average, root angle difference, and root angle geometric mean were evaluated and correlated to disease severity. A genome wide association study (GWAS) using the Fixed and random model Circulating Probability Unification (FarmCPU) statistical method, identified five associated single nucleotide polymorphisms (SNPs) for disease severity and two SNPs for biomass. The SNPs were found on Pv03, Pv07, Pv08, Pv10, and Pv11. One candidate gene for disease reaction near a SNP on Pv03 codes for a peroxidase, and two candidates associated with biomass SNPs were a 2-alkenal reductase gene cluster on Pv10 and a Pentatricopeptide repeat domain on Pv11. Bean lines utilized in the study were ranked by genomic estimated breeding values (GEBV) for disease severity, biomass, and the root architecture traits, and the observed and predicted values had high to moderate correlations. Cross validation of genomic predictions showed slightly lower correlational accuracy. Bean lines with the highest GEBV were among the most resistant, but did not necessarily rank at the very top numerically. This study provides information on the relationship of root architecture traits to root rot disease reaction. Snap bean lines with genetic merit for genomic selection were identified and may be utilized in future breeding efforts.

A Toolkit to Rapidly Modify Root Systems Through Single Plant Selection

Background: The incorporation of root traits into elite germplasm is typically a slow process. Thus, innovative approaches are required to accelerate research and pre-breeding programs targeting root traits to improve yield stability in different environments and soil types. Marker-assisted selection (MAS) can help to speed up the process by selecting key genes or quantitative trait loci (QTL) associated with root traits. However, this approach is limited due to the complex genetic control of root traits and the limited number of well-characterised large effect QTL. Coupling MAS with phenotyping could increase the reliability of selection. Here we present a useful framework to rapidly modify root traits in elite germplasm. In this wheat exemplar, a single plant selection (SPS) approach combined three main elements: phenotypic selection (in this case for seminal root angle); MAS using KASP markers (targeting a root biomass QTL); and speed breeding to accelerate each cycle.Results: To develop a SPS approach that integrates non-destructive screening for seminal root angle and root biomass, two initial experiments were conducted. Firstly, we demonstrated that transplanting wheat seedlings from clear pots (for seminal root angle assessment) into sand pots (for root biomass assessment) did not impact the ability to differentiate genotypes with high and low root biomass. Secondly, we demonstrated that visual scores for root biomass were correlated with root dry weight (r = 0.73), indicating that single plants could be evaluated for root biomass in a non-destructive manner. To highlight the potential of the approach, we applied SPS in a backcrossing program which integrated MAS and speed breeding for the purpose of rapidly modifying the root system of elite bread wheat line Borlaug100. Bi-directional selection for root angle in segregating generations successfully shifted the mean root angle by 30o in the subsequent generation (P ≤ 0.05). Within 18 months, BC2F4:F5 introgression lines were developed that displayed a full range of root configurations, while retaining similar above-ground traits to the recurrent parent. Notably, the seminal root angle displayed by introgression lines varied more than 30° compared to the recurrent parent, resulting in lines with both narrow and wide root angles, and high and low root biomass phenotypes.Conclusion: The SPS approach enables researchers and plant breeders to rapidly manipulate root traits of future crop varieties, which could help improve productivity in the face of increasing environmental fluctuations. The newly developed elite wheat lines with modified root traits provide valuable materials to study the value of different root systems to support yield in different environments and soil types.