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Development of First Multiparent Advanced Generation Inter-cross (MAGIC) Population in Pigeonpea (Cajanus cajan)

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Pigeonpea is the sixth most important legume crop in the world and it is a rich source of proteins. Conventional methods of breeding varieties with higher yield and inbuilt resistance are time consuming and cumbersome process. Molecular breeding with the help of genome wide sequence information will be helpful in achieving the goal in less time with high precision.
24 June 2015

Development of First Multiparent Advanced Generation Inter-cross (MAGIC) Population in Pigeonpea (Cajanus cajan)

  1. 1. Pigeonpea is the sixth most important legume crop in the world and it is a rich source of proteins. Conventional methods of breeding varieties with higher yield and inbuilt resistance are time consuming and cumbersome process. Molecular breeding with the help of genome wide sequence information will be helpful in achieving the goal in less time with high precision. With an aim to enhance genetic gains and to identify genomic regions responsible for economically important traits in pigeonpea a first set of multiparent advanced generation inter-cross mapping population (MAGIC) is being developed. Eight parental genotypes are being used for crossing and for assessment of marker polymorphism for testing hybridity, of F1s. As a first step of development (two-way crosses) a total of 28 two-way cross have been developed in current cropping season 2012 - 2013. Presently, re-sequencing of 8 parent lines is in under progress to identify the polymorphic SNP between parental lines. In the subsequent year we will complete the 14 four-way crosses and 7 eight-way crosses. The lines generated through eight way crosses will be advanced through single seed decent method to generate the 500 MAGIC lines. These lines will be phenotyped for disease screening and yield and yield related traits under multi-location trials. The phenotypic data together with genotypic data will be used to identify the marker trait associations (MTA) for the targeted traits and can be further used in marker assisted selection for pigeonpea improvement. Financial support from United States Agency for International Development is gratefully acknowledged. The authors thank Swathi Parulpalli and Kishan Patel (ICRISAT). ICRISAT is a member of the CGIAR Consortium. Abstract Acknowledgements Generation of F1s Description of parents used in MAGIC MAGIC Scheme Whole genome re-sequencing of parental lines Summary Vikas K Singh1, Rachit K Saxena1, Vinay Kumar1, CV Sameer Kumar1, Suyash Patil1, Mayank Kaashyap1, V Suryanarayana1, K B Saxena1, Rajeev K Varshney1,2,* 1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India 2Generation Challenge Programme, CIMMYT, Mexico, DF, Mexico, *Address for correspondence: r.k.varshney@cgiar.org Development of First Multiparent Advanced Generation Inter-cross (MAGIC) Population in Pigeonpea (Cajanus cajan) Genotypes Features ICP 7426 High pod numbers, medium duration HPL 24 High protein content, medium duration, compact, susceptible to FW and resistant to SMD, inter-specific derivative ICP 11605 Early flowering, germplasm line ICP 14209 High number of pods, germplasm line ICP 14486 Early flowering, germplasm line ICP 5529 Medium duration, obcordate leaves, compact plant, poor yielding, modified flower ICP 7035 Medium duration, SMD resistant to both Patancheru and Bangalore races, large purple seed, high sugar content ICP 8863 Erect, mid late, highly resistant to FW and susceptible to SMD, an extensively grown variety in Northern Karnataka and Maharashtra region of India, red seeded genotype ICP 7426 HPL 24 ICP 11605 ICP 14209 ICP 14486 ICP 5529 ICP 7035 ICP 8863 ICP 7426 HPL 24 24 ICP 11605 45 37 ICP 14209 60 32 30 ICP 14486 45 20 34 45 ICP 5529 20 10 10 15 16 ICP 7035 50 26 30 70 50 20 ICP 8863 32 35 30 20 27 10 80 Developed MAGIC lines will be used for phenotyping to identify the marker trait association (MTA) for target traits. Total of 28 two way crosses were attempted in the net house conditions. Numbers of F1s seed generated (28 combination) Identification of polymorphic SSR between parents  DNA libraries of all eight MAGIC parental lines for whole genome re-sequencing on MiSeq platform have been constructed. Sequencing of samples is performed at minimum of 5X coverage. Whole genome re-sequencing for one parental lines ICP 8863 has been completed successfully on MiSeq platform being used using 2 X150 bp pair-end sequencing. Re-sequencing of rest seven parental lines is in under progress.  SNPs and haplotypes will be identified among parental lines. Genomic DNA 1 2 3 4 5 6 7 8 Before size selection After size selection Bioanalyzer profile of DNA library of selected sample showed average size of 450 bp. 1 ICP 7426 2 HPL 24 3 ICP 11605 4 ICP 14209 5 ICP 14486 6 ICP 5529 7 ICP 7035 8 ICP 8863 L 1 2 3 4 L 5 6 7 8 L L 1 2 3 4 L 5 6 7 8 L Sequencing of sample on MiSeq platform A A BB C C DD E E F F H HXX X G G X AB X CD EF X GH ABCD EFGH ABCDEFGH CS-1 CS-2 CS-3 CS-4CS-5CS-n Half di-allele mating of 8 founder MAGIC line Selfing n cycle through single seed decent method Generation of 14, 4-way crosses (AEGH, AHCE…..) Generation of 7, 8-way crosses, (ADGHFGCE, AFGCDBEH……….) Selfing to generate F2 Population (500 plants ≈ 72 plants from each 8 way crosses) Generation of 500 MAGIC Lines Generation of 28, 2-way crosses (AB, AC, AD, AE, AF, AG, AH…..) M 1 2 3 4 5 6 7 8 M 1 2 3 4 5 6 7 8 M: 100 bp DNA ladder; 1: ICP7426; 2: HPL24; 3: ICP 11605; 4: ICP 14209; 5: ICP14486; 6: ICP5529; 7: ICP7035; 8: ICP8863 CcM306 CcM602 DNA Library preparation for Pair-end sequencing on MiSeq platform
  • KanchanJadhav6

    Feb. 27, 2020
  • BharatPatidar8

    Mar. 19, 2018
  • BehailuMulugeta

    Jul. 23, 2017

Pigeonpea is the sixth most important legume crop in the world and it is a rich source of proteins. Conventional methods of breeding varieties with higher yield and inbuilt resistance are time consuming and cumbersome process. Molecular breeding with the help of genome wide sequence information will be helpful in achieving the goal in less time with high precision. 24 June 2015

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