plant omics journal

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Articles 2025 | 17(02): 2025

Genome-scale mining of simple sequence repeats (SSRs) in the forage grass Urochloa mosambicensis using low-coverage whole-genome sequencing data: abundance, distribution, and composition

Ueslei Silva Leão*, Geice Ribeiro da Silva, Luíce Gomes Bueno, Aline Barbosa Negreiros, and Fábio Mendonça Diniz*

Universidade Estadual do Piauí, UESPI, São Raimundo Nonato PI 64770-000, Brazil
Northeast Biotechnology Network - RENORBIO/Animal Science Program - PPGCA, Universidade Federal do Piauí, Teresina PI 64049-550, Brazil
Embrapa Gado de Corte, Avenida Rádio Maia, 830, Zona Rural, 79106-550, Campo Grande, MS, Brazil
Embrapa Caprinos e Ovinos, Sobral CE 62010-970, Brazil

Abstract
Simple sequence repeats (SSRs), also known as microsatellites, are common components of prokaryotic and eukaryotic genomes. Microsatellite loci are widely applied as molecular marker systems in plant population studies and genetic breeding due to their codominant inheritance, high polymorphism, and reproducibility. The development of these markers, however, requires prior genomic information. Although low-coverage whole-genome sequencing using the Illumina MiSeq platform provides limited sequencing depth, it is usually sufficient to identify thousands of SSR regions. In this study, low-coverage sequencing was performed on the Urochloa mosambicensis genome using the Illumina MiSeq platform. This tropical forage grass shows strong potential for adaptability and persistence in dry environments, making it a promising feed source for ruminants in harsh conditions. The U. mosambicensis genome was screened for SSRs to evaluate their potential for molecular marker development. The high-quality Illumina sequencing reads were assembled into 32,931 contigs (N50 = 395 bp) using the CLC Genomics Workbench. The software Krait and MSDB were used to analyze the low-coverage U. mosambicensis sequencing data in order to identify and evaluate pure, interrupted pure, compound, and interrupted compound SSRs. A total of 2,665 pure microsatellites were identified, with the highest relative abundances found in trinucleotides (31.52 loci/Mb) and pentanucleotides (16.62 loci/Mb). Hexanucleotides (87.18%) and trinucleotides (86.96%) exhibited the highest proportion of sequences suitable for amplification. A greater abundance of interrupted compound motifs (1.81 loci/Mb) and pure compound SSRs (1.15 loci/Mb) was observed compared to interrupted pure SSRs (0.48 loci/Mb). This study also suggests that non-consensus bases positively influence the size of interrupted pure microsatellites, indicating greater stability against potential mutations. These findings provide a valuable resource for the selection of potential molecular markers for genetic breeding and population studies of the tropical forage species U. mosambicensis.

Pages 1-11 | Full Text PDF| doi: 10.21475/POJ.17.02.25.p18

Articles 2025 | 17(01): 2025

Effect of temperature on seed germination of five hemp (Cannabis sativa L.) cultivars from Rif Mountains (northern Morocco)

Ismail El Bakali*, Soufian Chakkour, Samir El Bakali, Mohamed Kadiri, Abderrahmane Merzouki

Laboratory of Applied Botany, Department of Biology, Faculty of Sciences of Tetouan, Abdelmalek Essaâdi University, Mhannech II. 93002, Tetouan, Morocco
Laboratory of Biology, Ecology, and Health, FS, Abdelamlek Essaadi University, Mhannech II. 93002, Tetouan, Morocco
Marine Ecotoxicology Team, Department of chemistry, Faculty of Sciences of Tetouan, Abdelmalek Essaâdi University, Mhannech II. 93002, Tetouan, Morocco

Abstract: Seed germination is a critical early factor influencing crop yield and quality. Hamp (Cannabis sativa) seed germination is significantly affected by changes in temperature and light conditions. This study investigates the effect of temperature on the germination of five cannabis cultivars from the Fifi region (northwestern Morocco), specifically ‘Beldiya’, ‘Mexicana’, ‘Khardala’, ‘Avocat’, and ‘Critical Plus’. We examined how temperature impacts several agro-biological parameters, including the final germination percentage (FGP), total germination time (TGT), mean germination time (MGT), mean daily germination (MDG), and latent life span (LLS). Our findings show that high temperatures (30°C) adversely affect all germination parameters across cultivars. The optimal FGP was observed within the 20°C to 25°C range for all cultivars. As temperature increases, germination accelerates, reducing TGT by 4 to 6 days depending on the cultivar. Rising temperatures also decrease MGT, grouping the cultivars into two response categories. In response to temperature shifts from 10°C to 25°C, ‘Beldiya’, ‘Mexicana’, and ‘Critical Plus’ exhibited significant reductions in MGT by 1.90, 1.83, and 1.80 days, respectively. ‘Khardala’ and ‘Avocat’ responded moderately, with decreases of 1.41 and 1.50 days. Higher temperatures also boosted MDG across all cultivars. At 10°C, MDG values increased by a factor of 2.4 for ‘Beldiya’, 2.6 for ‘Khardala’ and ‘Avocat’, 3.4 for ‘Critical Plus’, and 4 for ‘Mexicana’. Furthermore, increasing temperatures shortened the LLS, advancing germination. Between 10°C and 25°C, ‘Mexicana’ and ‘Critical Plus’ advanced germination by 2.8 to 3.5 days, while ‘Avocat’, ‘Beldiya’, and ‘Khardala’ advanced by 1.7 to 1.8 days. Overall, the local cultivars demonstrated better adaptation to local environmental conditions compared to newly introduced varieties.

Submitted: 25/05/2024 | Revised: 28/12/2024 | Accepted: 29/12/2024

Pages 1-9 | Read Article| Full Text PDF| doi: 10.21475/POJ.17.01.25.p06
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Seed quality of white oats with different foliar applications of zinc

Marta Gubert Tremea, Guilherme Roberto Schalanski, Gerusa Massuquini Conceição, José Antonio Gonzalez da Silva, Maria Eduarda Schmidt, Cibele Luisa Peter, Laura Eduarda Arnold, Joeli Vaz Bagolin

Federal University de Pelotas, Brasil
Northwest Regional University of the State of Rio Grande do Sul, Brasil

Abstract: The objective of this study was to evaluate the physiological quality of white oat seeds produced through foliar biofortification with zinc. The experiment was conducted in the experimental area of the Regional Institute for Rural Development (IRDeR), where white oats were sown and biofortified with zinc at doses of 0, 1000, 2000, and 4000 g ha⁻¹, applied at two different physiological stages of the plants, constituting a completely randomized experimental design with two factors. The analyzed variables were seed yield, thousand-seed weight, first germination count, germination, accelerated aging, seedling length, seedling dry mass, and electrical conductivity. The application of zinc through foliar biofortification only influenced yield when more than one application was performed, resulting in above-average outcomes, i.e., greater than 1600 kg ha⁻¹. For seed quality, the number of zinc applications did not differ statistically; however, different zinc doses had a significant influence on the first germination count, germination, accelerated aging, and seedling length tests, as well as on yield components, demonstrating the effectiveness of using foliar zinc biofortification for both the quantity and quality of white oat seed production.

Submitted: 18/06/2024 | Revised: 07/10/2024 | Accepted: 08/10/2024

Pages 10-13 | Read Article| Full Text PDF| doi: 10.21475/POJ.17.01.25.p13