Harnessing genetic potential of wheat germplasm banks through impact-oriented-prebreeding for future food and nutritional security.

Uttam Kumar, Vaibhav K Singh, Sanjay Singh, Sajid Shokat, Mian A R Arif, Khalil A Laghari, Puja Srivastava, Sridhar Bhavani, Satish Kumar, Dharam Pal, Jai P Jaiswal, Kai Sonder, Harinder K Chaudhary, Jose Crossa, Thomas S Payne, Muhammad Imtiaz, Virinder S Sohu, Gyanendra P Singh, Navtej S Bains, Anthony Hall, Kevin V Pixley, Ernesto Solis-Moya, Prashant Vikram, Deepmala Sehgal, Juan Burgueño, Achla Sharma, Sanjay K Singh, Carolina P Sansaloni, Ryan Joynson, Thomas Brabbs, Cynthia Ortiz, Sukhwinder Singh, Velu Govindan, Naveen Gupta, Harminder S Sidhu, Ashwani K Basandrai, Daisy Basandrai, Lourdes Ledesma-Ramires, Maria P Suaste-Franco, Guillermo Fuentes-Dávila, Javier I Moreno

Journal: Scientific reports 2019;8(1):12527

PMID: 30131572

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Abstract

The value of exotic wheat genetic resources for accelerating grain yield gains is largely unproven and unrealized. We used next-generation sequencing, together with multi-environment phenotyping, to study the contribution of exotic genomes to 984 three-way-cross-derived (exotic/elite1//elite2) pre-breeding lines (PBLs). Genomic characterization of these lines with haplotype map-based and SNP marker approaches revealed exotic specific imprints of 16.1 to 25.1%, which compares to theoretical expectation of 25%. A rare and favorable haplotype (GT) with 0.4% frequency in gene bank identified on chromosome 6D minimized grain yield (GY) loss under heat stress without GY penalty under irrigated conditions. More specifically, the 'T' allele of the haplotype GT originated in Aegilops tauschii and was absent in all elite lines used in study. In silico analysis of the SNP showed hits with a candidate gene coding for isoflavone reductase IRL-like protein in Ae. tauschii. Rare haplotypes were also identified on chromosomes 1A, 6A and 2B effective against abiotic/biotic stresses. Results demonstrate positive contributions of exotic germplasm to PBLs derived from crosses of exotics with CIMMYT's best elite lines. This is a major impact-oriented pre-breeding effort at CIMMYT, resulting in large-scale development of PBLs for deployment in breeding programs addressing food security under climate change scenarios.

Address: International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico. [email protected].; International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico.; Department Plant Breeding & Genetics, Punjab Agriculture University, Ludhiana, 141004, India.; ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India.; Earlham Institute, Norwich, Norfolk, NR4 7UG, UK.; Carretera Celaya-San Miguel de Allende, Km 0.6.5, C.P., 38110, Celaya, Guanajuato, Mexico.; Borlaug Institute for South Asia (BISA), CIMMYT, Ladhowal, Punjab, 141004, India.; CSK Himachal Pradesh Agricultural University Palampur, Palampur, Himachal Pradesh, 176062, India.; INIFAP-CIRNO, Campo Experimental Norman E. Borlaug, Apdo. Postal 155, Km 12 Norman E. Borlaug, Cd. Obregon, Sonora, C.P., 85000, Mexico.; INIFAP, Interior Parque Los Colomos S/N, Colonia Providencia, CP, 44660, Guadalajara, Jalisco, Mexico.; ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110 012, India.; National Research Center for Plant Biotechnology, New Delhi, 110 012, India.; Nuclear Institute for Agriculture and Biology, Faislabad, 38000, Pakistan.; Department of Plant and Environmental Sciences, Crop Science, University of Copenhagen, Højbakkegård Allé 13, DK-2630, Taastrup, Denmark.; Nuclear Institute of Agriculture, Tando Jam, Sindh, 70050, Pakistan.; CIMMYT - World Agroforestry Centre (ICRAF), United Nations Avenue, Gigiri. P.O. Box 1041-00621, Nairobi, Kenya.; ICAR-Indian Agricultural Research Institute, Regional Station, Shimla, 171004, India.; Department of Genetics and Plant Breeding, G.B. Pant University of Agriculture & Technology, Pantnagar, 263145, Uttarakhand, India.; CIMMYT - Pakistan, NARC CSI Complex, Park Road, Islamabad, 44000, Pakistan.; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.; International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco, C.P., 56237, Mexico. [email protected].

DOI: 10.1038/s41598-018-30667-4

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MeSH Terms: Chromosome Mapping, Edible Grain, Food Supply, Gene Frequency, Haplotypes, High-Throughput Nucleotide Sequencing, Hot Temperature, Plant Breeding, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Seed Bank, Sequence Analysis, DNA, Stress, Physiological, Triticum