Potential of (GATA)n microsatellites from rice for inter- and intra-specific variability studies

Davierwala, Armaity P.; Ramakrishna, Wusirika; Chowdari, Venkat; Ranjekar, P. K.; Gupta, Vidya S.

doi:10.1186/1471-2148-1-7

Cited by 15 publications

(5 citation statements)

References 78 publications

(79 reference statements)

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“…(GA) 8 YG was earlier reported to be one of the most informative primers for studying diversity in rice landraces and wild species (Sarla et al, 2003;. The primer (GATA) 4 could help distinguish all the 12 varieties and is suitable for use in fingerprinting as reported earlier for rice and tomato (Davierwala et al, 2001;Rao et al, 2006).…”

Section: Discussionmentioning

confidence: 81%

“…Inter-simple sequence repeat (ISSR) markers based on AG and GA repeats have been reported to be very informative and cost-effective in determining genetic relationships among diverse accessions of rice germplasm (Olufowote et al, 1997;Garland et al, 1999;Joshi et al, 2000;Davierwala et al, 2000;Sarla et al, 2003;, and have been shown to be very useful in different steps of the breeding process (Reddy et al, 2002). (GATA) n containing loci were reported to be useful in fingerprinting of rice (Davierwala et al, 2001) and tomato (Rao et al, 2006). There is increasing interest in presence of GA repeats in promoters and their role in gene regulation (Santi et al, 2003;Zhang et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

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ISSR markers based on GA and AG repeats reveal genetic relationship among rice varieties tolerant to drought, flood, or salinity

Reddy

Babu

Swamy

et al. 2009

J. Zhejiang Univ. Sci. B

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Drought, flood, salinity, or a combination of these limits rice production. Several rice varieties are well known for their tolerance to specific abiotic stresses. We determined genetic relationship among 12 rice varieties including 9 tolerant to drought, flood, or salinity using inter-simple sequence repeat (ISSR) markers. Based on all markers, the nine tolerant varieties formed one cluster distinct from the cluster of three control varieties. The salt-tolerant varieties were closest to two flood-tolerant varieties, and together they were distinct from the drought-tolerant varieties. (GA)(8)YG was the most informative primer, showing the highest polymorphic information content (PIC) and resolving power (Rp). The drought-, flood-, and salt-tolerant varieties grouped in three distinct clusters within the group of tolerant varieties, when (GA)(8)YG was used. Sabita was the only exception. The two aus varieties, Nagina22 and FR13A, were separated and grouped with the drought- and flood-tolerant varieties, respectively, but they were together in dendrograms based on other primers. The results show that ISSR markers associated with (GA)(8)YG delineated the three groups of stress-tolerant varieties from each other and can be used to identify genes/new alleles associated with the three abiotic stresses in rice germplasm.

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Section: Discussionmentioning

confidence: 81%

Section: Introductionmentioning

confidence: 99%

ISSR markers based on GA and AG repeats reveal genetic relationship among rice varieties tolerant to drought, flood, or salinity

Reddy

Babu

Swamy

et al. 2009

J. Zhejiang Univ. Sci. B

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“…In this investigation, the C. sinensis GATA protein family was systematically evaluated to explore the characteristics and expression patterns of these transcription factors to evaluate their importance as regulators of CBC resistance. A total of 24 CsGATAs encoded in the C. sinensis genome were identified, suggesting that sweet orange plants encode fewer GATAs than other plant species [ 1 , 3 , 5 , 6 , 7 , 8 ]. A lot of research has been conducted on GATAs as regulators of growth, development, and responses to abiotic stressors; however, far less is known about their influence on biotic stress responses.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, based on the conserved domains, Arabidopsis thaliana B-GATA proteins can be further subclassified into the N-terminal HAN domain and Cterminal LLM domain [4]. To date, many GATA gene family members have been classified by systematic annotation, such as 30,28,64,28,30,96,31,49, and 79 members of the GATA members have been annotated in Arabidopsis [5], rice [6], soybean [7], millet [3], tomato [1], rapeseed [8], Phyllostachys pubescens [9], potato [10], and wheat [11], respectively. These gene families offer a valuable reference to further explore the biological characteristics and functions of members of this GATA transcription factor family.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Characterization of the Sweet Orange (Citrus sinensis) GATA Family Reveals a Role for CsGATA12 as a Regulator of Citrus Bacterial Canker Resistance

Fan,

Xian,

Huang

et al. 2024

IJMS

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Citrus bacterial canker (CBC) is a severe bacterial infection caused by Xanthomonas citri subsp. citri (Xcc), which continues to adversely impact citrus production worldwide. Members of the GATA family are important regulators of plant development and regulate plant responses to particular stressors. This report aimed to systematically elucidate the Citrus sinensis genome to identify and annotate genes that encode GATAs and evaluate the functional importance of these CsGATAs as regulators of CBC resistance. In total, 24 CsGATAs were identified and classified into four subfamilies. Furthermore, the phylogenetic relationships, chromosomal locations, collinear relationships, gene structures, and conserved domains for each of these GATA family members were also evaluated. It was observed that Xcc infection induced some CsGATAs, among which CsGATA12 was chosen for further functional validation. CsGATA12 was found to be localized in the nucleus and was differentially upregulated in the CBC-resistant and CBC-sensitive Kumquat and Wanjincheng citrus varieties. When transiently overexpressed, CsGATA12 significantly reduced CBC resistance with a corresponding increase in abscisic acid, jasmonic acid, and antioxidant enzyme levels. These alterations were consistent with lower levels of salicylic acid, ethylene, and reactive oxygen species. Moreover, the bacteria-induced CsGATA12 gene silencing yielded the opposite phenotypic outcomes. This investigation highlights the important role of CsGATA12 in regulating CBC resistance, underscoring its potential utility as a target for breeding citrus varieties with superior phytopathogen resistance.

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“…As a result, developments in DNA molecular markers and their capacity to identify genomic areas linked with significant features would be more beneficial (e.g., drought tolerance). ISSR markers are useful because they offer a rapid, accurate, and comprehensive method that may also be utilized to develop genetic and genomic fingerprinting [57]. ISSR markers were employed herein to measure the genetic diversity and to identify the prospective crosses by comparing these parents at the molecular level.…”

Section: Discussionmentioning

confidence: 99%

Biochemical, Anatomical, Genetic, and Yield Assessment of Seven Rice Genotypes (Oryza sativa L.) Subjected to Drought Stress

Abo-Youssef,

Elbagory,

Elsehely

et al. 2023

Agronomy

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Drought stress is one of the main environmental challenges that dramatically reduce global rice production within several agricultural ecosystems. Breeding drought-tolerant rice genotypes is an important sustainable strategy to overcome this constraint. In this work, drought tolerance levels were assessed according to biochemical, anatomical, and molecular aspects, which led to selecting three promising crosses (Sakha 107 × Sakha super 300, Sakha 107 × M206, and Sakha 107 × Sakha 108) that were compared with their parents as controls. The antioxidant capabilities of the chosen potential crosses, such as the ascorbate peroxidase activity (APX), superoxide dismutase activity (SOD), catalase activity (CAT), and total phenolics, were significantly higher compared with their parents under drought stress. Moreover, the promising selected crosses could accumulate greater proline and chlorophyll contents. The potential superiority of the three selected rice crosses was anatomically represented throughout cross-sections of roots, stems, and leaves, which recorded higher values of cross-section diameter, epidermal thickness, cortex thickness, mesophyll thickness, and bundle sheath thickness as well as a broader range of xylem vessel diameters than their parents under a water deficit. The observed superiority of the antioxidant activities in the overall drought-tolerance mechanisms and anatomical characteristics reflected their protective role in the adaptation process under water stress. Molecular analyses using inter-simple sequence repeat (ISSR) markers suggested two promising crosses (Sakha 107 × Sakha super 300 and Sakha 107 × M206) to be the most suitable crosses for saving water. They had the highest similarity values and were grouped in a distinct cluster. The relative gene expression of OsACS2, OsCML31, OsCYP94C2a, and OsSRO1c was significantly elevated in the two selected drought-tolerant rice genotypes (Sakha 107 × Sakha super 300 and Sakha 107 × M206).

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Potential of (GATA)n microsatellites from rice for inter- and intra-specific variability studies

Abstract: Background: The microsatellite, (GATA) n has been frequently used for DNA fingerprinting. However, very few attempts have been made to analyze (GATA) n -containing loci in rice.

Cited by 15 publications

References 78 publications

ISSR markers based on GA and AG repeats reveal genetic relationship among rice varieties tolerant to drought, flood, or salinity

ISSR markers based on GA and AG repeats reveal genetic relationship among rice varieties tolerant to drought, flood, or salinity

Genome-Wide Identification and Characterization of the Sweet Orange (Citrus sinensis) GATA Family Reveals a Role for CsGATA12 as a Regulator of Citrus Bacterial Canker Resistance

Biochemical, Anatomical, Genetic, and Yield Assessment of Seven Rice Genotypes (Oryza sativa L.) Subjected to Drought Stress

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