Selective InDel marker identification across the peanut ( Arachis hypogaea L.) genome using ddRADSeq

被引：0
作者：
Qureshi, Moin [1 ]
Guden, Birgul [1 ]
Tosun, Hilal Sule [2 ]
Kordrostami, Mojtaba [3 ]
Gangurde, Sunil S. [4 ]
Uzun, Bulent [1 ]
Yol, Engin [1 ]
机构：
[1] Akdeniz Univ, Fac Agr, Dept Field Crops, Antalya, Turkiye
[2] Akdeniz Univ, Fac Agr, Dept Plant Protect, Antalya, Turkiye
[3] Nucl Sci & Technol Res Inst NSTRI, Nucl Agr Res Sch, Karaj, Iran
[4] Int Crops Res Inst Semi Arid Trop, Hyderabad, India
来源：
TURKISH JOURNAL OF BOTANY | 2024年 / 48卷 / 07期
关键词：
Groundnut; peanut; InDel markers; ddRADSeq; genetic diversity; marker-assisted breeding; EVOLUTION; CHICKPEA; DNA; YIELD; ACID;
D O I：
10.55730/1300-008X.2826
中图分类号：
Q94 [植物学];
学科分类号：
071001 ;
摘要：
The advent of next-generation sequencing technologies, and particularly double digest restriction site-associated DNA sequencing (ddRADSeq), has significantly advanced the development of molecular markers for crop genetics. This study used ddRADSeq to identify and develop insertion-deletion (InDel) markers in 25 peanut genotypes from diverse geographical regions. The bioinformatic analysis revealed 62,728 InDels across the peanut genome, predominantly between 1 and 5 bp, which constituted 96% of the total, while InDels of >= 6 bp accounted for 3.96%. We focused on 1013 InDels of at least 10 bp for further analysis, representing 1.61% of the total reads, with a distribution of 832 insertions and 181 deletions. Of those, 21 InDels were selected for primer design and successfully amplified to produce markers within the range of 150-400 bp. Approximately 9.5% of the InDels were located in coding sequences, enhancing their potential utility in genomics-led breeding. These markers' polymorphic information content varied from 0 to 0.371, demonstrating substantial genetic diversity with an average value of 0.163. These findings confirm the effectiveness of ddRADSeq for InDel marker development in peanuts, illustrating its potential to enhance marker-assisted breeding programs by providing robust tools for assessing genetic diversity.
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收藏
页码：441 / 453
页数：17
相关论文
共 65 条
  • [1] Basak M, Uzun B, Yol E, Genetic diversity and population structure of the Mediterranean sesame core collection with use of genome-wide SNPs developed by double digest RAD-Seq, PLoS One, 14, 10, (2019)
  • [2] Batley J, Barker G, O'Sullivan H, Edwards KJ, Edwards D, Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data, Plant Physiology, 132, 1, pp. 84-91, (2003)
  • [3] Bennetzen JL, Wang H, The contributions of transposable elements to the structure, function, and evolution of plant genomes, Annual Review of Plant Biology, 65, pp. 505-530, (2014)
  • [4] Bertioli DJ, Cannon SB, Froenicke L, Huang G, Farmer AD, Et al., The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut, Nature Genetics, 48, 4, pp. 438-446, (2016)
  • [5] Bhat RS, Shirasawa K, Chavadi SD, Genome‐wide structural and functional features of single nucleotide polymorphisms revealed from the whole genome resequencing of 179 accessions of Arachis, Physiologia Plantarum, 174, 1, (2022)
  • [6] Bhat RS, Shirasawa K, Gangurde SS, Rashmi MG, Sahana K, Et al., Genome-wide landscapes of genes and repeatome reveal the genomic differences between the two subspecies of peanut (Arachis hypogaea), Crop Design, 2, 1, (2023)
  • [7] Britten RJ, Rowen L, Williams J, Cameron RA, Majority of divergence between closely related DNA samples is due to indels, Proceedings of the National Academy of Sciences, 100, 8, pp. 4661-4665, (2003)
  • [8] Chen ZJ, Sreedasyam A, Ando A, Song Q, De Santiago LM, Et al., Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement, Nature Genetics, 52, 5, pp. 525-533, (2020)
  • [9] Chen W, Zhang L, The pattern of DNA cleavage intensity around indels, Scientific Reports, 5, 1, (2015)
  • [10] Cortaga CQ, Lachica JAP, Lantican DV, Ocampo ETM, Genome-wide SNP and InDel analysis of three Philippine mango species inferred from whole-genome sequencing, Journal of Genetic Engineering and Biotechnology, 20, 1, (2022)
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