Dataset Information

Identification of novel QTL governing root architectural traits in an interspecific soybean population.

ABSTRACT: Cultivated soybean (Glycine max L.) cv. Dunbar (PI 552538) and wild G. soja (PI 326582A) exhibited significant differences in root architecture and root-related traits. In this study, phenotypic variability for root traits among 251 BC2F5 backcross inbred lines (BILs) developed from the cross Dunbar/PI 326582A were identified. The root systems of the parents and BILs were evaluated in controlled environmental conditions using a cone system at seedling stage. The G. max parent Dunbar contributed phenotypically favorable alleles at a major quantitative trait locus on chromosome 8 (Satt315-I locus) that governed root traits (tap root length and lateral root number) and shoot length. This QTL accounted for >10% of the phenotypic variation of both tap root and shoot length. This QTL region was found to control various shoot- and root-related traits across soybean genetic backgrounds. Within the confidence interval of this region, eleven transcription factors (TFs) were identified. Based on RNA sequencing and Affymetrix expression data, key TFs including MYB, AP2-EREBP and bZIP TFs were identified in this QTL interval with high expression in roots and nodules. The backcross inbred lines with different parental allelic combination showed different expression pattern for six transcription factors selected based on their expression pattern in root tissues. It appears that the marker interval Satt315-I locus on chromosome 8 contain an essential QTL contributing to early root and shoot growth in soybean.

SUBMITTER: Manavalan LP

PROVIDER: S-EPMC4355624 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Identification of novel QTL governing root architectural traits in an interspecific soybean population.

Manavalan Lakshmi P LP Prince Silvas J SJ Musket Theresa A TA Chaky Julian J Deshmukh Rupesh R Vuong Tri D TD Song Li L Cregan Perry B PB Nelson James C JC Shannon J Grover JG Specht James E JE Nguyen Henry T HT

PloS one 20150310 3

Cultivated soybean (Glycine max L.) cv. Dunbar (PI 552538) and wild G. soja (PI 326582A) exhibited significant differences in root architecture and root-related traits. In this study, phenotypic variability for root traits among 251 BC2F5 backcross inbred lines (BILs) developed from the cross Dunbar/PI 326582A were identified. The root systems of the parents and BILs were evaluated in controlled environmental conditions using a cone system at seedling stage. The G. max parent Dunbar contributed ...[more]

PMID: 25756528

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Project description:Agronomically important traits generally have complex genetic architecture, where many genes have a small and largely additive effect. Genomic prediction has been demonstrated to increase genetic gain and efficiency in plant breeding programs beyond marker-assisted selection and phenotypic selection. The objective of this study was to evaluate the impact of allelic origin, marker density, training population size, and cross-validation schemes on the accuracy of genomic prediction models in an interspecific soybean nested association mapping (NAM) panel. Three cross-validation schemes were used: (a) Within-Family (WF): training population and predictions are made exclusively within each family; (b) Across All families (AF): all the individuals from the three families were randomly assigned to either the training or validation set; (c) Leave one Family out (LFO): each family is predicted using a training set that contains the other two families. Predictive abilities increased with training population size up to 350 individuals, but no significant gains were noted beyond 250 individuals in the training population. The number of markers had a limited impact on the observed predictive ability across traits; increasing markers used in the model above 1000 revealed no significant increases in prediction accuracy. Predictive abilities for AF were not significantly different from the WF method, and predictive abilities across populations for the WF method had a range of 0.58 to 0.70 for maturity, protein, meal, and oil. Our results also showed encouraging prediction accuracies for grain yield (0.58–0.69) using the WF method. Partitioning genomic prediction between G. max and G. soja alleles revealed useful information to select material with a larger allele contribution from both parents and could accelerate allele introgression from exotic germplasm into the elite soybean gene pool. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01203-6.

Project description:Background and aimsPlant roots growing underground are critical for soil resource acquisition, anchorage and plant-environment interactions. In wheat ( Triticum aestivum ), however, the target root traits to improve yield potential still remain largely unknown. This study aimed to identify traits of seedling root system architecture (RSA) associated with yield and yield components in 226 recombinant inbred lines (RILs) derived from a cross between the bread wheat Triticum aestivum 'Forno' (small, wide root system) and spelt Triticum spelta 'Oberkulmer' (large, narrow root system).MethodsA 'pouch and wick' high-throughput phenotyping pipeline was used to determine the RSA traits of 13-day-old RIL seedlings. Two field experiments and one glasshouse experiment were carried out to investigate the yield, yield components and phenology, followed by identification of quantitative trait loci (QTLs).Key resultsThere was substantial variation in RSA traits between genotypes. Seminal root number and total root length were both positively associated with grains m -2 , grains per spike, above-ground biomass m -2 and grain yield. More seminal roots and longer total root length were also associated with delayed maturity and extended grain filling, likely to be a consequence of more grains being defined before anthesis. Additionally, the maximum width of the root system displayed positive relationships with spikes m -2 , grains m -2 and grain yield. Ten RILs selected for the longest total roots exhibited the same effects on yield and phenology as described above, compared with the ten lines with the shortest total roots. Genetic analysis revealed 38 QTLs for the RSA, and QTL coincidence between the root and yield traits was frequently observed, indicating tightly linked genes or pleiotropy, which concurs with the results of phenotypic correlation analysis.ConclusionsBased on the results from the Forno × Oberkulmer population, it is proposed that vigorous early root growth, particularly more seminal roots and longer total root length, is important to improve yield potential, and should be incorporated into wheat ideotypes in breeding.

Dataset Information

Identification of novel QTL governing root architectural traits in an interspecific soybean population.

Publications

Identification of novel QTL governing root architectural traits in an interspecific soybean population.

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