[논문]InDel markers: An extended marker resource for molecular breeding in chickpea

Jain, Ankit; Roorkiwal, Manish; Kale, Sandip; Garg, Vanika; Yadala, Ramakrishna; Varshney, Rajeev K.

doi:10.1371/journal.pone.0213999

[해외논문] InDel markers: An extended marker resource for molecular breeding in chickpea 원문보기

PloS one, v.14 no.3, 2019년, pp.e0213999 -

Jain, Ankit (International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India) , Roorkiwal, Manish (International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India) , Kale, Sandip (International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India) , Garg, Vanika (International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India) , Yadala, Ramakrishna (International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India) , Varshney, Rajeev K. (International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India)

Abstract ▼ AI-Helper

Chickpea is one of the most important food legumes that holds the key to meet rising global food and nutritional demand. In order to deploy molecular breeding approaches in crop improvement programs, user friendly and cost effective marker resources remain prerequisite. The advent of next generation sequencing (NGS) technology has resulted in the generation of several thousands of markers as part of several large scale genome sequencing and re-sequencing initiatives. Very recently, PCR based Insertion-deletions (InDels) are becoming a popular gel based genotyping solution because of their co-dominant, inexpensive, and highly polymorphic nature. With an objective to expand marker resources for genomics assisted breeding (GAB) in chickpea, whole genome re-sequencing data generated on five parental lines of one interspecific (ICC 4958 × PI 489777) and two intra-specific (ICC 283 × ICC 8261 and ICC 4958 × ICC 1882) mapping populations, were used for identification of InDels. A total of 231,658 InDels were identified using Dindel software with default parameters. Further, a total of 8,307 InDels with ≥20 bp size were selected for development of gel based markers, of which primers could be designed for 7,523 (90.56%) markers. On average, markers appeared at a frequency of 1,038 InDels/LG with a maximum number of markers on CaLG04 (1,952 InDels) and minimum on CaLG08 (360 InDels). In order to validate these InDels, a total of 423 primer pairs were randomly selected and tested on the selected parental lines. A high amplification rate of 80% was observed ranging from 46.06 to 58.01% polymorphism rate across parents on 3% agarose gel. This study clearly reflects the usefulness of available sequence data for the development of genome-wide InDels in chickpea that can further contribute and accelerate a wide range of genetic and molecular breeding activities in chickpea.

참고문헌 (47)

1 Varshney RK , Song C , Saxena RK , Azam S , Yu S , Sharpe AG , et al Draft genome sequence of chickpea ( Cicer arietinum ) provides a resource for trait improvement . Nat. Biotechnol . 2013 ; 31 : 240 – 246 . 10.1038/nbt.2491 23354103

상세보기
2 Croser JS , Ahmad F , Clarke HJ , Siddique KHM . Utilisation of wild Cicer in chickpea improvement—progress, constraints, and prospects . Crop Pasture Sci . 2003 ; 54 : 429 – 444 .
3 Jukanti AK , Gaur PM , Gowda CLL , Chibbar RN . Nutritional quality and health benefits of chickpea ( Cicer arietinum L.): a review . Br. J. Nutr . 2012 ; 108 : S12 – S26 .
4 Gan Y , Johnston AM , Diane Knight J , McDonald C , Stevenson C . Nitrogen dynamics of chickpea: Effects of cultivar choice, N fertilization, Rhizobium inoculation, and cropping systems . Can. J. Plant Sci . 2010 ; 90 : 655 – 666 .

상세보기
5 Saraf CS , Rupela OP , Hegde DM , Yadav RL , Shivkumar BG , Bhattarai S , et al Biological nitrogen fixation and residual effects of winter grain legumes in rice and wheat cropping systems of the Indo-Gangetic Plain In: Residual effects of legumes in rice and wheat cropping systems of the Indo-Gangetic plain , Kumar Rao JVDK , Johansen C , and Rego TJ , Eds., Oxford & IBH Publishing Co Pvt Ltd , New Delhi ; 1998 ; pp. 14 – 30 .
6 Ramirez ML , Cendoya E , Nichea MJ , Zachetti VGL , Chulze SN . Impact of toxigenic fungi and mycotoxins in chickpea: a review . Curr. Opin. Food Sci . 2018 ; 23 : 32 – 37 .
7 Kashiwagi J , Krishnamurthy L , Purushothaman R , Upadhyaya HD , Gaur PM , Gowda CLL , et al Scope for improvement of yield under drought through the root traits in chickpea ( Cicer arietinum L.) . Field Crops Res . 2015 ; 170 : 47 – 54 .

상세보기
8 Varshney RK , Graner A , Sorrells ME . Genomics-assisted breeding for crop improvement . Trends Plant Sci . 2005 ; 10 : 621 – 630 . 10.1016/j.tplants.2005.10.004 16290213

상세보기
9 Kole C , Muthamilarasan M , Henry R , Edwards D , Sharma R , Abberton M , et al Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects . Front. Plant Sci . 2015 ; 6 : 563 10.3389/fpls.2015.00563 26322050

상세보기
10 Roorkiwal M , Jain A , Thudi M , Varshney RK . Advances in Chickpea Genomic Resources for Accelerating the Crop Improvement In: The Chickpea Genome , Varshney et al (eds.), Springer International Publishing 2017 pp. 53 – 68 .
11 Vasemägi A , Gross R , Palm D , Paaver T , Primmer CR . Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon . BMC Genomics 2010 ; 11 : 156 10.1186/1471-2164-11-156 20210987

상세보기
12 Lovett ST . Encoded errors: mutations and rearrangements mediated by misalignment at repetitive DNA sequences . Mol. Microbiol . 2004 ; 52 : 1243 – 1253 . 10.1111/j.1365-2958.2004.04076.x 15165229

상세보기
13 Mullaney JM , Mills RE , Pittard WS , Devine SE . Small insertions and deletions (INDELs) in human genomes . Human Mol. Genet . 2010 ; 19 : R131 – R136 . 20858594
14 Terakami S , Matsumura Y , Kurita K , Kanamori H , Katayose Y , Yamamoto T , et al Complete sequence of the chloroplast genome from pear ( Pyrus pyrifolia ): genome structure and comparative analysis . Tree Genet. Genomes 2012 ; 8 : 841 – 854 .
15 Rockah-Shmuel L , Tóth-Petróczy Á , Sela A , Wurtzel O , Sorek R , Tawfik DS . Correlated occurrence and bypass of frame-shifting insertion-deletions (InDels) to give functional proteins . PLoS Genet . 2013 ; 9 : e1003882 10.1371/journal.pgen.1003882 24204297

상세보기
16 Newman TL , Tuzun E , Morrison VA , Hayden KE , Ventura M , McGrath SD , et al A genome-wide survey of structural variation between human and chimpanzee . Genome Res . 2005 ; 15 : 1344 – 1356 . 10.1101/gr.4338005 16169929

상세보기
17 Mills RE , Luttig CT , Larkins CE , Beauchamp A , Tsui C , Pittard WS , et al An initial map of insertion and deletion (INDEL) variation in the human genome . Genome Res . 2006 ; 16 : 1182 – 1190 . 10.1101/gr.4565806 16902084

상세보기
18 Wu DH , Wu HP , Wang CS , Tseng HY , Hwu KK . Genome-wide InDel marker system for application in rice breeding and mapping studies . Euphytica 2013 ; 192 : 131 – 143 .

상세보기
19 Păcurar DI , Păcurar ML , Street N , Bussell JD , Pop TI , Gutierrez L , et al A collection of INDEL markers for map-based cloning in seven Arabidopsis accessions . J. Exp. Bot . 2012 ; 63 : 2491 – 2501 . 10.1093/jxb/err422 22282537

상세보기
20 Zhou G , Zhang Q , Tan C , Zhang X , Li C . Development of genome-wide InDel markers and their integration with SSR, DArT and SNP markers in single barley map . BMC Genomics 2015 ; 16 : 804 10.1186/s12864-015-2027-x 26474969

상세보기
21 Yang J , Wang Y , Shen H , Yang W . In silico identification and experimental validation of insertion-deletion polymorphisms in tomato genome . DNA Res . 2014 ; 21 : 429 – 438 . 10.1093/dnares/dsu008 24618211

상세보기
22 Li W , Cheng J , Wu Z , Qin C , Tan S , Tang X , et al An InDel-based linkage map of hot pepper ( Capsicum annuum ) . Mol. Breed . 2015 ; 35 : 32 10.1007/s11032-015-0219-3 25620878

상세보기
23 Moghaddam SM , Song Q , Mamidi S , Schmutz J , Lee R , Cregan P , et al Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L . Front. Plant Sci . 2014 ; 5 : 185 10.3389/fpls.2014.00185 24860578

상세보기
24 Liu B , Wang Y , Zhai W , Deng J , Wang H , Cui Y , et al Development of InDel markers for Brassica rapa based on whole-genome re-sequencing . Theor. Appl. Genet . 2013 ; 126 : 231 – 239 . 10.1007/s00122-012-1976-6 22972202

상세보기
25 Wu K , Yang M , Liu H , Tao Y , Mei J , Zhao Y . Genetic analysis and molecular characterization of Chinese sesame ( Sesamum indicum L.) cultivars using insertion-deletion (InDel) and simple sequence repeat (SSR) markers . BMC Genet . 2014 ; 15 : 35 10.1186/1471-2156-15-35 24641723

상세보기
26 Jain M , Misra G , Patel RK , Priya P , Jhanwar S , Khan AW , et al A draft genome sequence of the pulse crop chickpea ( Cicer arietinum L.) . Plant J . 2013 ; 74 : 715 – 729 . 10.1111/tpj.12173 23489434

상세보기
27 Gupta S , Nawaz K , Parween S , Roy R , Sahu K , Kumar Pole A , et al Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement . DNA Res . 2016 ; 24 : 1 – 10 .
28 Thudi M , Khan AW , Kumar V , Gaur PM , Katta K , Garg V , et al Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea ( Cicer arietinum L.) . BMC Plant Biol . 2016 ; 16 : 10 10.1186/s12870-015-0690-3 26822060

상세보기
29 Thudi M , Chitikineni A , Liu X , He W , Roorkiwal M , Yang W , et al Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea ( Cicer arietinum L.) . Sci. Rep . 2016 ; 6 : 38636 10.1038/srep38636 27982107

상세보기
30 Cuc LM , Mace ES , Crouch JH , Quang VD , Long TD , Varshney RK . Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut ( Arachis hypogaea ) . BMC Plant Biol . 2008 ; 8 : 55 10.1186/1471-2229-8-55 18482440

상세보기
31 Li H , Durbin R . Fast and accurate short read alignment with Burrows-Wheeler Transform . Bioinformatics 2009 ; 25 : 1754 – 1760 . 10.1093/bioinformatics/btp324 19451168

상세보기
32 Albers CA , Lunter G , MacArthur DG , McVean G , Ouwehand WH , Durbin R . Dindel: accurate indel calls from short-read data . Genome Res . 2011 ; 21 : 961 – 973 . 10.1101/gr.112326.110 20980555

상세보기
33 Rozen S , Skaletsky H . Primer3 on the WWW for general users and for biologist programmers . Methods Mol. Biol . 2000 ; 132 : 365 – 386 . 10547847
34 Varshney RK , Gaur PM , Chamarthi SK , Krishnamurthy L , Tripathi S , Kashiwagi J , et al Fast-track introgression of QTL-hotspot for root traits and other drought tolerance traits in JG 11, an elite and leading variety of chickpea . Plant Genome 2013 ; 6 : 1 – 9 10.3835/plantgenome2013.07.0022

상세보기
35 Varshney RK , Mohan SM , Gaur PM , Chamarthi SK , Singh VK , Samineni S , et al Marker-assisted backcrossing to introgress resistance to Fusarium wilt (FW) race 1 and Ascochyta blight (AB) in C 214, an elite cultivar of chickpea . Plant Genome 2014 ; 7 : 1 – 11 10.3835/plantgenome2013.10.0035

상세보기
36 Pratap A , Chaturvedi SK , Tomar R , Rajan N , Malviya N , Thudi M , et al Marker-assisted introgression of resistance to fusarium wilt race 2 in Pusa 256, an elite cultivar of desi chickpea . Mol. Genet. Genomics 2017 ; 292 : 1237 – 1245 . 10.1007/s00438-017-1343-z 28668975

상세보기
37 Roorkiwal M , Rathore A , Das RR , Singh MK , Jain A , Srinivasan S , et al Genome-enabled prediction models for yield related traits in chickpea . Front. Plant Sci . 2016 ; 7 : 1666 10.3389/fpls.2016.01666 27920780

상세보기
38 Roorkiwal M , Jarquin D , Singh MK , Gaur PM , Bharadwaj C , Rathore A , et al Genomic-enabled prediction models using multi-environment trials to estimate the effect of genotype × environment interaction on prediction accuracy in chickpea . Sci. Rep . 2018 ; 8 : 11701 10.1038/s41598-018-30027-2 30076340

상세보기
39 Das S , Upadhyaya HD , Srivastava R , Bajaj D , Gowda CLL , Sharma S , et al Genome-wide insertion–deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications in chickpea . DNA Res . 2015 ; 22 : 377 – 386 . 10.1093/dnares/dsv020 26385353

상세보기
40 Srivastava R , Singh M , Bajaj D , Parida SK . A high-resolution InDel (insertion–deletion) markers-anchored consensus genetic map identifies major QTLs governing pod number and seed yield in chickpea . Front. Plant Sci . 2016 ; 7 : 1362 10.3389/fpls.2016.01362 27695461

상세보기
41 Ridge S , Deokar A , Lee R , Daba K , Macknight RC , Weller JL , et al The chickpea early flowering 1 (Efl1) locus is an ortholog of Arabidopsis ELF3 . Plant Physiol . 2017 175 : 802 – 815 10.1104/pp.17.00082 28818860

상세보기
42 Roorkiwal M , Jain A , Kale SM , Doddamani D , Chitikineni A , Thudi M , et al Development and evaluation of high density SNP array ( Axiom CicerSNP Array) for high resolution genetic mapping and breeding applications in chickpea . Plant Biotechnol. J . 2018 ; 16 : 890 – 901 . 10.1111/pbi.12836 28913885

상세보기
43 Varshney RK , Thudi M , Nayak SN , Gaur PM , Kashiwagi J , Krishnamurthy L , et al Genetic dissection of drought tolerance in chickpea ( Cicer arietinum L.) . Theor. Appl. Genet . 2014 ; 127 : 445 – 462 . 10.1007/s00122-013-2230-6 24326458

상세보기
44 Jaganathan D , Thudi M , Kale S , Azam S , Roorkiwal M , Gaur PM , et al Genotyping-by-sequencing based intra-specific genetic map refines a “ QTL-hotspot ” region for drought tolerance in chickpea . Mol. Gen. Genomics 2015 ; 290 : 559 – 571 .

상세보기
45 Salathia N , Lee HN , Sangster TA , Morneau K , Landry CR , Schellenberg K , et al Indel arrays: an affordable alternative for genotyping . Plant J . 2007 ; 51 : 727 – 737 . 10.1111/j.1365-313X.2007.03194.x 17645438

상세보기
46 Hou X , Li L , Peng Z , Wei B , Tang S , Ding M , et al A platform of high-density INDEL/CAPS markers for map-based cloning in Arabidopsis . Plant J . 2010 ; 63 : 880 – 888 . 10.1111/j.1365-313X.2010.04277.x 20561258

상세보기
47 Jiang J , Gao Y , Hou Y , Li W , Zhang S , Zhang Q , et al Whole-genome resequencing of Holstein bulls for Indel discovery and identification of genes associated with milk composition traits in dairy cattle . PloS One 2016 ; 11 : e0168946 10.1371/journal.pone.0168946 28030618

상세보기

표제어: PCR

동의어: Packet Collision Rate

용어 설명 출처 목록 (6)

용어 설명: PCR은 세균 특이성이 있는 primer를 이용하여 적은 수의 세균이 있을지라도 쉽게 검출할 수 있는 유용한 방법이며, 이를 이용하여 구강 내 치면세균막이나 타액에서 직접 세균을 검출할 수 있게 되었다[8].

내보내기 구분	파일저장 인쇄 메일전송
구성항목	기본정보 상세정보 관리번호, 논문명, 저널/프로시딩명, 저자 , 발행년, 권, 호, 시작페이지, 끝페이지, 발행기관 관리번호, 논문명, 대등논문명, 저자 , 저널/프로시딩명, 발행기관, 발행년, 발행언어, 권, 호, 시작페이지, 끝페이지, ISBN, ISSN, 주제분야, 키워드, 초록(한글), 초록(영문), 저자(소속기관)
저장형식	Text(ASCII format) Excel format RefWorks Direct Export RIS format (for Reference Manager, ProCite, EndNote), Scholar's Aids, Mendeley
메일정보	받는사람 (필수) @ 보내는사람 (선택) @ 제목 내용 KISTI 검색결과 이메일 서비스
안내	총 건의 자료가 검색되었습니다. 다운받으실 자료의 인덱스를 입력하세요. (1-10,000) 검색결과의 순서대로 최대 10,000건 까지 다운로드가 가능합니다. 데이타가 많을 경우 속도가 느려질 수 있습니다.(최대 2~3분 소요) 다운로드 파일은 UTF-8 형태로 저장됩니다. 파일의 내용이 제대로 보이지 않을실 때는 웹브라우저 상단의 보기 -> 인코딩 -> 자동선택 여부를 확인하십시오. ~ Text(ASCII format) Excel format

연합인증

[해외논문] InDel markers: An extended marker resource for molecular breeding in chickpea 원문보기

Abstract ▼ AI-Helper

참고문헌 (47)

이 논문을 인용한 문헌

관련 콘텐츠

원문 보기

원문 URL 링크

오픈액세스(OA) 유형

이 논문과 함께 이용한 콘텐츠

AI-Helper ※ AI-Helper는 오픈소스 모델을 사용합니다.

선택된 텍스트