Root system architecture variation among barley (Hordeum vulgare L.) accessions at seedling stage under soil acidity condition.

MAIN CONCLUSION: Soil acidity in Ethiopian highlands impacts barley production, affecting root system architecture. Study on 300 accessions showed significant trait variability, with potential for breeding enhancement. Soil acidity poses a significant challenge to crop production in the highland regions of Ethiopia, particularly impacting barley, a crucial staple crop. This acidity serves as a key stressor affecting the root system architecture (RSA) of this crop. Hence, the objective of this study was to assess the RSA traits variability under acidic soil conditions using 300 barley accessions in a greenhouse experiment. The analysis of variance indicated substantial variations among the accessions across all traits studied. The phenotypic coefficient of variation ranged from 24.4% for shoot dry weight to 11.1% for root length, while the genotypic coefficient variation varied between 18.83 and 9.2% for shoot dry weight and root length, respectively. The broad-sense heritability ranged from 36.7% for leaf area to 69.9% for root length, highlighting considerable heritability among multiple traits. The genetic advances as a percent of the mean ranged from 13.63 to 29.9%, suggesting potential for enhancement of these traits through breeding efforts. Principal component analysis and cluster analysis grouped the genotypes into two major clusters, each containing varying numbers of genotypes with contrasting traits. This diverse group presents an opportunity to access a wide range of potential parent candidates to enhance genetic variablity in breeding programs. The Pearson correlation analysis revealed significant negative associations between root angle (RA) and other RSA traits. This helps indirect selection of accessions for further improvement in soil acidity. In conclusion, this study offers valuable insights into the RSA characteristics of barley in acidic soil conditions, aiding in the development of breeding strategies to enhance crop productivity in acidic soil environments.

Multi-locus genome-wide association study reveal genomic regions underlying root system architecture traits in Ethiopian sorghum germplasm.

The identification of genomic regions underlying the root system architecture (RSA) is vital for improving crop abiotic stress tolerance. To improve sorghum (Sorghum bicolor L. Moench) for environmental stress tolerance, information on genetic variability and genomic regions linked to RSA traits is paramount. The aim of this study was, therefore, to investigate common quantitative trait nucleotides (QTNs) via multiple methodologies and identify genomic regions linked to RSA traits in a panel of 274 Ethiopian sorghum accessions. Multi-locus genome-wide association study was conducted using 265,944 high-quality single nucleotide polymorphism markers. Considering the QTN detected by at least three different methods, a total of 17 reliable QTNs were found to be significantly associated with root angle, number, length, and dry weight. Four QTNs were detected on chromosome SBI-05, followed by SBI-01 and SBI-02 with three QTNs each. Among the 17 QTNs, 11 are colocated with previously identified root traits quantitative trait loci and the remaining six are genome regions with novel genes. A total of 118 genes are colocated with these up- and down-streams of the QTNs. Moreover, five QTNs were found intragenic. These QTNs are S5_8994835 (number of nodal roots), S10_55702393 (number of nodal roots), S1_56872999 (nodal root angle), S9_1212069 (nodal root angle), and S5_5667192 (root dry weight) intragenic regions of Sobic.005G073101, Sobic.010G198000, Sobic.001G273000, Sobic.009G013600, and Sobic.005G054700, respectively. Particularly, Sobic.005G073101, Sobic.010G198000, and Sobic.009G013600 were found responsible for the plant growth hormone-induced RSA. These genes may regulate root development in the seedling stage. Further analysis on these genes might be important to explore the genetic structure of RSA of sorghum.

Genome-wide association study reveals genomic loci influencing agronomic traits in Ethiopian sorghum (Sorghum bicolor (L.) Moench) landraces.

Uncovering the genetic basis of agronomic traits in sorghum landraces that have adapted to various agro-climatic conditions would contribute to sorghum improvement efforts around the world. To identify quantitative trait nucleotides (QTNs) associated with nine agronomic traits in a panel of 304 sorghum accessions collected from diverse environments across Ethiopia (considered to be the center of origin and diversity), multi-locus genome-wide association studies (ML-GWAS) were performed using 79,754 high quality single nucleotide polymorphism (SNP) markers. Association analyses using six ML-GWAS models identified a set of 338 significantly (LOD ≥ 3)-associated QTNs for nine agronomic traits of sorghum accessions evaluated in two environments (E1 and E2) and their combined dataset (Em). Of these, 121 reliable QTNs, including 13 for flowering time (DF), 13 for plant height (PH), 9 for tiller number (TN), 15 for panicle weight (PWT), 30 for grain yield per panicle (GYP), 12 for structural panicle mass (SPM), 13 for hundred seed weight (HSW), 6 for grain number per panicle (GNP), and 10 for panicle exertion (PE) were consistently detected by at least three ML-GWAS methods and/or in two different environments. Notably, Ethylene responsive transcription factor gene AP2/ERF, known for regulation of plant growth, and the sorghum Terminal flower1/TF1 gene, which functions in the control of floral architecture, were identified as strong candidate genes associated with PH and HSW, respectively. This study provides an entry point for further validation studies to elucidate complex mechanisms controlling important agronomic traits in sorghum. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01381-5.

Natural variation further increases resilience of sorghum bred for chronically drought-prone environments.

Drought stress is one of the major constraints for crop production in the Sahel region of Africa. Here, we explore the potential to use natural genetic variation to build on the inherent drought tolerance of an elite sorghum cultivar, Teshale, that has been bred for Ethiopian conditions including chronic drought. We evaluated a backcross nested-association mapping population using 12 diverse founder lines crossed with Teshale under three drought-prone environments in Ethiopia. All 12 populations averaged higher head exsertion and lower leaf senescence than the recurrent parent in the two most stressful environments, reflecting new drought resilience mechanisms from the donors. A total of 154 quantitative trait loci (QTLs) were detected for eight drought-responsive traits, and their validity was supported by the fact that 113 (73.4%) overlapped with QTLs previously detected for the same traits, concentrated in regions previously associated with 'stay-green' traits. Allele effects showed that some favourable alleles are already present in the Ethiopian cultivar; however, the exotic donors offer rich scope for increasing drought resilience. Using model-selected SNPs associated with the eight traits identified in this study and three in a companion study, phenotypic prediction accuracies for grain yield were equivalent to genome-wide SNPs and were significantly better than random SNPs, indicating that the selected traits are predictive of sorghum grain yield.

Genetic diversity, population structure, and selection signature in Ethiopian sorghum [Sorghum bicolor L. (Moench)] germplasm.

Ethiopia, the probable center of origin and diversity for sorghum [Sorghum bicolor L. (Moench)] and with unique ecogeographic features, possesses a large number of sorghum landraces that have not been well studied. Increased knowledge of this diverse germplasm through large-scale genomic characterization may contribute for understanding of evolutionary biology, and adequate use of these valuable resources from the center of origin. In this study, we characterized genetic diversity, population structure and selection signature in 304 sorghum accessions collected from diverse sorghum growing regions of Ethiopia using genotyping-by-sequencing. We identified a total of 108,107 high-quality single-nucleotide polymorphism (SNPs) markers that were evenly distributed across the sorghum genome. The average gene diversity among accessions was high (He = 0.29). We detected a relatively low frequency of rare alleles (26%), highlighting the potential of this germplasm for subsequent allele mining studies through genome-wide association studies. Although we found no evidence of genetic differentiation among administrative regions (FST = 0.02, P = 0.12), population structure and cluster analyses showed clear differentiation among six Ethiopian sorghum populations (FST = 0.28, P = 0.01) adapting to different environments. Analysis of SNP differentiation between the identified genetic groups revealed a total of 40 genomic regions carrying signatures of selection. These regions harbored candidate genes potentially involved in a variety of biological processes, including abiotic stress tolerance, pathogen defense and reproduction. Overall, a high level of untapped diversity for sorghum improvement remains available in Ethiopia, with patterns of diversity consistent with divergent selection on a range of adaptive characteristics.

A database of simple sequence repeats from cereal and legume expressed sequence tags mined in silico: survey and evaluation.

Simple sequence repeats (SSRs) or microsatellites are an important class of molecular markers for genome analysis and plant breeding applications. In this paper, the SSR distributions within ESTs from the legumes soybean (Glycine max, representing 135.86 Mb), medicago (Medicago truncatula, 121.1 Mb) and lotus (Lotus japonicus, 45.4 Mb) have been studied relative to the distributions in cereals such as sorghum (Sorghum bicolor, 98.9 Mb), rice (Oryza sativa, 143.9 Mb) and maize (Zea mays, 183.7 Mb). The relative abundance, density, composition and putative annotations of di-, tri-, tetra- and penta-nucleotide repeats have been compared and SSR containing ESTs (SSR-ESTs) have been clustered to give a non-redundant set of EST-SSRs, available in a database. Further, a subset of such candidate EST-SSRs from sorghum have been tested for their ability to detect polymorphism between Striga-susceptible, stay-green drought tolerant mapping population parent 'E 36-1' and its Striga-resistant, non-stay-green counterpart 'N13'. Primer sets for 64% of the EST-SSRs tested produced a clear and specific PCR product band and 34% of these detected scorable polymorphism between the N13 and E 36-1 parental lines. Over half of these markers have been genotyped on 94 RILs from the (N13 x E 36-1)-based mapping population, with 42 markers mapping onto the ten sorghum linkage groups. This establishes the value of this database as a resource of molecular markers for practical applications in cereal and legume genetics and breeding. The primer pairs for non-redundant EST-SSRs have been designed and are freely available through the database (http://intranet.icrisat.org/gt1/ssr/ssrdatabase.html).