Development of a panel of unigene-derived polymorphic EST–SSR markers in lentil using public database information

Gupta, Debjyoti Sen; Peng, Cheng; Sablok, Gaurav; Thavarajah, Dil; Thavarajah, Pushparajah; Coyne, Clarice J.; Kumar, Shiv; Baum, Michaël; McGee, Rebecca J.

doi:10.1016/j.cj.2016.06.012

Cited by 11 publications

(4 citation statements)

References 37 publications

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“…Subsequently, the use of RFLP markers remained limited in lentil because it required high technical skills for their development. The advent of markers based on PCR (random amplified polymorphic DNA [RAPD], sequence characterized amplified region [SCAR], and SSR) has accelerated their use widely in lentil breeding programs (Kumar et al, 2015), and they are still in use (A. Singh et al, 2016; Ates, Aldemir, Alsaleh, et al, 2018; D. Singh et al, 2016; D. Singh et al, 2019; Gupta et al, 2016; Kumar, Choudhary, et al, 2018; Kumar, Gupta, Biradar, et al, 2018; Mbasani‐Mansi et al, 2019; Polanco et al, 2019; Tsanakas et al, 2018). In lentil, a set of 122 genomic SSR markers were developed for utilization in breeding programs (Verma et al, 2014).…”

Section: Acceleration In the Development Of Genomic Resources For Elevating Lentil From Orphan Statusmentioning

confidence: 99%

Genomics‐assisted lentil breeding: Current status and future strategies

et al. 2021

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Genomics‐assisted breeding has become a powerful tool to develop high‐yielding climate‐resilient varieties for adaptation to adverse environmental conditions such as heat and drought stresses. Previously, efforts have been made to develop genomic resources in lentil, leading to the development of many trait‐specific mapping populations, cores and mini‐cores, and single nucleotide polymorphism and simple sequence repeat markers. Molecular markers have been used in genetic diversity analyses and to clarify genetic relationships in lentil. However, availability of cost‐effective next‐generation sequencing and genotyping‐by‐sequencing technologies has provided unprecedented opportunities for advancing genetics research and breeding applications. For instance, it has become possible to assemble the large and complex genome, develop high‐density genetic maps for high‐resolution QTL mapping, and deploy genome‐wide association study in lentil. Furthermore, a range of cost‐effective marker genotyping platforms have been developed. These developments offer ample opportunities to modernize current breeding programs in lentil for accelerating genetic gains. This review discusses the current status and future possibilities of genomics‐assisted breeding to develop and deploy lentil cultivars suitable for changing climatic conditions.

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Section: Acceleration In the Development Of Genomic Resources For Elevating Lentil From Orphan Statusmentioning

confidence: 99%

Genomics‐assisted lentil breeding: Current status and future strategies

et al. 2021

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“…culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp [ 1 ]. It is grown throughout the world, and Turkey is the fourth most important lentil producing country (365.000 tons annually) after Canada, Australia, and USA [ 2 ]. Average annual lentil production of world is now approaching 6 Mt and per capita consumption of lentil has been increasing faster than human population growth [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

A consensus linkage map of lentil based on DArT markers from three RIL mapping populations

et al. 2018

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BackgroundLentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes.Materials and methodsA consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including “CDC Redberry” x “ILL7502” (LR8), “ILL8006” x “CDC Milestone” (LR11) and “PI320937” x “Eston” (LR39).ResultsThe lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps.ConclusionThis high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.

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“…Primer pairs developed in a previous study ( Sen Gupta et al, 2016 ) were used to amplify the BHLH-1 gene in CDC Redberry genomic DNA. Optimum PCR conditions for BHLH-1 primer pairs in an ABI 7500 thermocylcer were established: 94°C for 5 min, followed by 30 cycles of 94°C for 1 min, 60°C for 1 min, 72°C for 1 min followed by a final elongation step of 72°C for 5 min.…”

Section: Resultsmentioning

confidence: 99%

“…One primer pair (FerrClo5) used for the development of qPCR compatible primers for the Ferritin gene in lentil. In addition, one primer pair specific to a lentil BHLH (Basic Helix Loop Helix) transcription factor or FER-like transcription factor gene sequence ( Sen Gupta et al, 2016 ) was synthesized. Primers were also designed for the iron-related transporter gene based on the IRT1 mRNA coding sequence (CDS) (LegumeIP database reference no.…”

Section: Methodsmentioning

confidence: 99%

Development of Molecular Markers for Iron Metabolism Related Genes in Lentil and Their Expression Analysis under Excess Iron Stress

Gupta

McPhee

Kumar³

2017

Front. Plant Sci.

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Multiple genes and transcription factors are involved in the uptake and translocation of iron in plants from soil. The sequence information about iron uptake and translocation related genes is largely unknown in lentil (Lens culinaris Medik.). This study was designed to develop iron metabolism related molecular markers for Ferritin-1, BHLH-1 (Basic helix loop helix), or FER-like transcription factor protein and IRT-1 (Iron related transporter) genes using genome synteny with barrel medic (Medicago truncatula). The second objective of this study was to analyze differential gene expression under excess iron over time (2 h, 8 h, 24 h). Specific molecular markers were developed for iron metabolism related genes (Ferritin-1, BHLH-1, IRT-1) and validated in lentil. Gene specific markers for Ferritin-1 and IRT-1 were used for quantitative PCR (qPCR) studies based on their amplification efficiency. Significant differential expression of Ferritin-1 and IRT-1 was observed under excess iron conditions through qPCR based gene expression analysis. Regulation of iron uptake and translocation in lentil needs further characterization. Greater emphasis should be given to development of conditions simulating field conditions under external iron supply and considering adult plant physiology.

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Development of a panel of unigene-derived polymorphic EST–SSR markers in lentil using public database information

Cited by 11 publications

References 37 publications

Genomics‐assisted lentil breeding: Current status and future strategies

Genomics‐assisted lentil breeding: Current status and future strategies

A consensus linkage map of lentil based on DArT markers from three RIL mapping populations

Development of Molecular Markers for Iron Metabolism Related Genes in Lentil and Their Expression Analysis under Excess Iron Stress

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