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Development of EST resources in pearl millet and their use in development and mapping of EST-SSRs in four RIL populations

By: Rajaram, V.
Contributor(s): Bhasker Raj, A.G [coaut.] | Blummel, M [coaut.] | Choudhary, S [coaut.] | Hash, C.T [coaut.] | Kavi Kishor, P.B [coaut.] | Kholova, J [coaut.] | Kocova, M [coaut.] | Kumar, S [coaut.] | Lakshmi Narasu. M [coaut.] | Nepolean, T [coaut.] | Pandurangarao, V [coaut.] | Rai, R.N [coaut.] | Sahrawat, K.L [coaut.] | Senthilvel, S [coaut.] | Singh, G [coaut.] | Supriya [coaut.] | Thakur, R.P [coaut.] | Vadez, V [coaut.] | Varshney, R.K [coaut.] | Yadav, R.C [coaut.] | Velu, G [coaut.] | Sharma, R.K [coaut.].
Material type: materialTypeLabelBookAnalytics: Show analyticsPublisher: 2010Description: 1 page.Summary: Elite pearl millet inbreds ICMB 841-P3 and 863B-P2 (RIL population parents differing for drought and salinity tolerance, downy mildew and blast resistance, and stover and grain quality) were drought stressed at boot-leaf stage using a standard dry-down protocol. Total RNA extracted separately from stressed root and leaf tissues of each inbred was used for cDNA synthesis. 454-sequencing of cDNAs yielded raw EST sequences that were cleaned and assembled using the PLANTTA pipeline. A total of 112,864 unigenes were obtained from the four cDNA samples. A total of 5,800 SNPs from 2,146 contigs were identified between the two parents. Similarly, 499 sequences containing class I SSRs were identified from the unigenes and from these 236 non-redundant EST-SSR primer pairs were designed. PCR products from 139 amplifying EST-SSR primer pairs and parental DNA of crosses ICMB 841-P3 x 863B-P2, H 77/833-2 x PRLT 2/89-33, 81B-P6 x ICMP 451-P8 and PT 732B-P2 x P1449-2-P1 were screened for polymorphism. >50 new EST-SSR markers were mapped for each mapping population and a consensus map developed. These four EST-SSR skeleton-mapped RIL populations have been phenotyped for grain Fe and Zn concentration, salinity tolerance, canopy conductance, downy mildew reaction, rust reaction, and/or blast reaction, and QTLs with closely flanking EST-SSR markers were detected for each of these traits. This study increases the number of mapped pearl millet SSRs by >40%, filling gaps in the earlier linkage maps, and will facilitate SSR-based marker-assisted foreground selection in parts of the pearl millet genome where this was not previously possible.Collection: CIMMYT Staff Publications Collection
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Conference proceedings CIMMYT Knowledge Center: John Woolston Library

Lic. Jose Juan Caballero Flores

 

CIMMYT Staff Publications Collection CIS-6163 (Browse shelf) Available
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Elite pearl millet inbreds ICMB 841-P3 and 863B-P2 (RIL population parents differing for drought and salinity tolerance, downy mildew and blast resistance, and stover and grain quality) were drought stressed at boot-leaf stage using a standard dry-down protocol. Total RNA extracted separately from stressed root and leaf tissues of each inbred was used for cDNA synthesis. 454-sequencing of cDNAs yielded raw EST sequences that were cleaned and assembled using the PLANTTA pipeline. A total of 112,864 unigenes were obtained from the four cDNA samples. A total of 5,800 SNPs from 2,146 contigs were identified between the two parents. Similarly, 499 sequences containing class I SSRs were identified from the unigenes and from these 236 non-redundant EST-SSR primer pairs were designed. PCR products from 139 amplifying EST-SSR primer pairs and parental DNA of crosses ICMB 841-P3 x 863B-P2, H 77/833-2 x PRLT 2/89-33, 81B-P6 x ICMP 451-P8 and PT 732B-P2 x P1449-2-P1 were screened for polymorphism. >50 new EST-SSR markers were mapped for each mapping population and a consensus map developed. These four EST-SSR skeleton-mapped RIL populations have been phenotyped for grain Fe and Zn concentration, salinity tolerance, canopy conductance, downy mildew reaction, rust reaction, and/or blast reaction, and QTLs with closely flanking EST-SSR markers were detected for each of these traits. This study increases the number of mapped pearl millet SSRs by >40%, filling gaps in the earlier linkage maps, and will facilitate SSR-based marker-assisted foreground selection in parts of the pearl millet genome where this was not previously possible.

Global Wheat Program

English

Lucia Segura

INT2983

CIMMYT Staff Publications Collection

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