Assessment of genetic diversity in salt-tolerant rice and its wild relatives for ten SSR loci and one allele mining primer of salT gene located on 1st chromosome

Ganie, Showkat Ahmad; Karmakar, Joydip; Roychowdhury, Rajib; Mondal, Tapan Kumar; Dey, Narottam

doi:10.1007/s00606-014-0999-7

Cited by 33 publications

(20 citation statements)

References 22 publications

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“…Several workers also reported that these markers are highly polymorphic (Mohammadi-nejad et al 2008;Karmakar et al 2012;Chattopadhyay et al 2014;Ganie et al 2014). The PCR profile obtained from the SSR markers generated a total of 99 alleles including 20 rare alleles and 16 null alleles, accounting an average of 12.37 alleles/ locus which is higher than the numbers reported by other groups using the SSR markers (Mohammadi-Nejad et al 2008;Islam et al 2012;Karmakar et al 2012;Das et al 2013).…”

Section: Discussionmentioning

confidence: 85%

Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes

Ganie

Borgohain

Kritika

et al. 2016

Physiol Mol Biol Plants

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Eight Saltol quantitative trait locus (QTL) linked simple sequence repeat (SSR) markers of rice (Oryza sativa L.) were used to study the polymorphism of this QTL in 142 diverse rice genotypes that comprised salt tolerant as well as sensitive genotypes. The SSR profiles of the eight markers generated 99 alleles including 20rare alleles and 16 null alleles. RM8094 showed the highest number (13) of alleles followed by RM3412 (12), RM562 (11), RM493 (9) and RM1287 (8) while as, RM10764 and RM10745 showed the lowest number (6) of alleles. Based on the highest number of alleles and PIC value (0.991), we identified RM8094 as suitable marker for discerning salt tolerant genotypes from the sensitive ones. Based upon the haplotype analysis using FL478 as a reference (salt tolerant genotypes containing Saltol QTL), we short listed 68 rice genotypes that may have at least one allele of FL478 haplotype. Further study may confirm that some of these genotypes might have Saltol QTL and can be used as alternative donors in salt tolerant rice breeding programmes.

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Section: Discussionmentioning

confidence: 85%

Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes

Ganie

Borgohain

Kritika

et al. 2016

Physiol Mol Biol Plants

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“…The use of CWR adapted for survival in extreme climatic conditions can be utilized for breeding crops which can grow in environments affected by climate change (Redden, ). Drought and salt tolerance in CWRs of wheat and barley (Naz et al ., ; Nevo and Chen, ; Verulkar et al ., ), rice (Amiri et al ., ; Feng et al ., ; Ganie et al ., ; Garg et al ., ; Michael and VanBuren, ), soya bean (Qi et al ., ) and brassica crops (Zhang et al ., c) among others are reported and can be utilized for this purpose.…”

Section: Applications Of Cwrsmentioning

confidence: 99%

Genomics of crop wild relatives: expanding the gene pool for crop improvement

Brożyńska

Furtado

Henry

2015

Plant Biotechnology Journal

331

216

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Summary Plant breeders require access to new genetic diversity to satisfy the demands of a growing human population for more food that can be produced in a variable or changing climate and to deliver the high‐quality food with nutritional and health benefits demanded by consumers. The close relatives of domesticated plants, crop wild relatives (CWRs), represent a practical gene pool for use by plant breeders. Genomics of CWR generates data that support the use of CWR to expand the genetic diversity of crop plants. Advances in DNA sequencing technology are enabling the efficient sequencing of CWR and their increased use in crop improvement. As the sequencing of genomes of major crop species is completed, attention has shifted to analysis of the wider gene pool of major crops including CWR. A combination of de novo sequencing and resequencing is required to efficiently explore useful genetic variation in CWR. Analysis of the nuclear genome, transcriptome and maternal (chloroplast and mitochondrial) genome of CWR is facilitating their use in crop improvement. Genome analysis results in discovery of useful alleles in CWR and identification of regions of the genome in which diversity has been lost in domestication bottlenecks. Targeting of high priority CWR for sequencing will maximize the contribution of genome sequencing of CWR. Coordination of global efforts to apply genomics has the potential to accelerate access to and conservation of the biodiversity essential to the sustainability of agriculture and food production.

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“…In general, rice plant is regarded as sensitive to salinity stress. High salinity stress causes severe impact on millions of hectares of agricultural land worldwide [ 1 , 2 ]. Accumulation of salts in the irrigated soil is one of the prime factors that lowers water availability to root cells of rice plants due to their reduced osmotic potential, hence diminish growth, development and yield of rice [ 3 , 4 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice

2017

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DUF221 domain-containing genes (DDP genes) play important roles in developmental biology, hormone signalling transduction, and responses to abiotic stress. Therefore to understand their structural and evolutionary relationship, we did a genome-wide analysis of this important gene family in rice. Further, through comparative genomics, DDP genes from Oryza sativa subsp. (indica), nine different wild species of rice and Arabidopsis were also identified. We also found an expansion of the DDP gene families in rice and Arabidopsis which is due to the segmental duplication events in some of the gene family members. In general, a highly purifying selection was found acting on all the deduced paralogous and orthologous DDP gene pairs. The data from microarray and subsequent qRT-PCR analysis revealed that although several OsDDPs were differentially regulated under salinity stress, yet OsDDP6 was upregulated at all the developmental stages in salt tolerant rice genotype, FL478. Interestingly, OsDDP6 was found to be involved in proline metabolism pathway as indicated by protein network analysis. The diverse gene structures, varied transmembrane topologies and the differential expression patterns implied the functional diversity in DDP genes. Therefore, the comprehensive evolutionary analysis of DDP genes from different Oryza species and Arabidopsis performed in this study will provide the basis for further functional validation studies vis-à-vis DDP genes of rice and other plant species.

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Assessment of genetic diversity in salt-tolerant rice and its wild relatives for ten SSR loci and one allele mining primer of salT gene located on 1st chromosome

Cited by 33 publications

References 22 publications

Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes

Assessment of genetic diversity of Saltol QTL among the rice (Oryza sativa L.) genotypes

Genomics of crop wild relatives: expanding the gene pool for crop improvement

Genome-wide analysis of DUF221 domain-containing gene family in Oryza species and identification of its salinity stress-responsive members in rice

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