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Genomics-enabled early generation selection in peanut breeding pipeline
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Genomics-enabled early generation selection in peanut breeding pipeline

  1. May 2019 Genomics-enabled early generation selection in peanut breeding pipeline MT Variath, SS Manohar, S Chaudhari, RK Varshney, MK Pandey, D Deshmukh, S Gattu, J Pasupuleti* International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India. * Corresponding authors: p.janila@cgiar.org About ICRISAT: www.icrisat.org ICRISAT’s scientific information: http://EXPLOREit.icrisat.org Context: Early generation selection in segregating peanut populations used markers linked to high oleic acid, rust and late leaf spot (LLS) resistance coupled with near-infrared reflectance spectroscopy (NIRS) for high oleic trait for selection decisions. Techniques such as rapid generation advancement, recycling of elite lines as parents, and early generation and multi-location testing in target sites resulted in an enhanced genetic gain for the high oleic trait. The significant outcomes are combining early maturity with foliar fungal disease resistance, and agronomically superior high oleic lines. For the 100-seed mass, a genetic gain of 17 g was achieved, from 35 g in 2015 to 52 g in 2017, through recycling of elite lines along with directional selection for seed size in the high oleic breeding pipeline. Superior performing high oleic as well as early maturing rust and LLS resistant lines are under national testing for release in India. Genomic-assisted breeding products ▪▪ The peanut breeding program uses MAS approach, although in the beginning MABC was used to improve the traits in popular cultivars. ▪▪ Developed high oleic varieties using Cleaved amplified polymorphic sequences (CAPS) and allele-specific markers associated with ahFAD2A and ahFAD2B mutant alleles conferring high oleic trait in peanut (Table 1). ▪▪ Successfully combined early maturity and resistance to LLS and rust using simple sequence repeat markers. Table 1. Cleaved amplified polymorphic sequences (CAPS) and allele-specific polymerase chain reaction (AS-PCR) markers for selecting ahFAD2A and ahFAD2B mutant alleles in breeding populations. Type of markers Linkage group Genes Markers Wild allele size (bp) Mutant allele size (bp) References Cleaved amplified polymorphic sequences (CAPS) A09 ahFAD2A aF19F and 1056R 598 and 228 826 Chu et al. (2009) B09 ahFAD2B bF19F and R1/ FADR 736, 263 and 171 550, 263, 213 and 171 Allele-specific polymerase chain reaction (AS-PCR) A09 ahFAD2A F435-F and F435SUB-R Null allele 203 Chen et al. (2010) B09 ahFAD2B F435-F and F435INS-R Null allele 195 Cost-effective SNP genotyping for early generation selection Table 3. Single nucleotide polymorphic (SNP) markers being used at ICRISAT for selection in early generations. SNP ID Trait Linkage group Genomic position (bp) Target allele Alternate allele Basis of SNP selection GKAMFAD2B High oleic trait B09 - A -:- Validated in the lab by CAPS marker GKAMA02GL582 Late leaf spot resistance A02 1271582 C G - GKAMA02GL975 A02 1156975 G C - GKAMA02GL829 A02 435829 C A NBS-LLR GKAMA02GL779 A02 436779 C T NBS-LLR GKAMA03QR786 Rust resistance A03 133497786 T A Validated in the lab by developing SSR markers GKAMA03QR517 A03 131739517 A C GKAMA03QR796 A03 131937796 G A GKAMA03QR661 A03 133527661 C G GKAMA03GR173 A03 134613173 G C Performance of 16 high oleic lines under multi-location evaluation trials during rainy 2016. Target sites for early generation and multi-location testing for high oleic, and early maturing LLS and rust resistance lines in India. The genetic gain for 100-seed mass in high oleic lines Large kernel size high oleic varieties with low oil content are preferred by the consumers and food industries. To cater the consumers and industry needs, elite parents were recycled in the breeding program and directional selection for the large kernel size in subsequent cycles was made to achieve a significant genetic gain for 100-seed mass from an average of 38 g in the lines developed in 2015 to 55 g in lines developed in 2017. The kernel size distribution that gives the proportion of the different sized kernels is another key criteria being used for advancement decisions in the breeding pipelines. Summary ▪▪ High oleic lines with superior yield were identified in Spanish and Virginia Bunch types. ▪▪ Recycling of elite lines in high oleic breeding pipelines resulted in improvement of agronomic and other traits besides high oleic trait. ▪▪ The network of testing sites of NARS partners enabled testing to fast track development of high oleic and early maturing foliar disease resistance lines. ▪▪ ICRISAT’s peanut breeding has shared over 100 high oleic peanut lines with partners in India, Bangladesh, Myanmar, Vietnam, Lao PDR, Senegal, Mali, Malawi, Tanzania, and Australia. Acknowledgment Department of Agriculture, Cooperation and Farmers’ Welfare, Government of India; OPEC Fund for International Development (OFID); The CGIAR Research Program on Grain Legumes and Dryland Cereals (CRP-GLDC); MARS Wringley Confectionery; Bill and Melinda Gates Foundation; Excellence in Breeding (EiB) Partners Indian Council of Agricultural Research-Directorate of Groundnut Research (ICAR-DGR), Junagadh, Gujarat, India;Department of Agricultural Research (DAR), Yezin, Myanmar;Bangladesh Agricultural Research Institute (BARI), Gazipur, Bangladesh; Vietnam Academy of Agricultural Sciences (VAAS), Thanh Tri, Vietnam; National Agriculture and Forestry Research Institute (NAFRI), Lao PDR State Agricultural Universities from India: Junagadh Agricultural University (JAU), Junagadh, Gujarat; Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, Telangana; Acharya N. G. Ranga Agricultural University (ANGRAU), Guntur, Andhra Pradesh; Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu; Mahatma Phule Krishi Vidyapeeth (MPKV), Rahuri, Maharashtra; University of Agricultural Science (UAS), Raichur, Karnataka; University of Agricultural Sciences, Dharwad, Karnataka. Kompetitive Allele Specific PCR (KASP) graph of SNP markers snpAH0021 associated with rust resistance showing allelic discrimination of homozygous resistant (blue dots), heterozygous types (green dots) and homozygous susceptible types (red dots). Genetic gain for 100-seed mass of high oleic lines developed in 2015, 16, 17 designated as ICGVs 15, 16 and 17 series evaluated over three years at ICRISAT. Around 10,000 individual plants are genotyped annually @2.5 $/samples including DNA isolation to make early generations selection decisions based on genotypic data The progress is underway to refine the existing SNP markers for LLS, design the chemistry for SNP markers of ahFAD2A and also to identify the new diagnostic SNP markers for fresh seed dormancy and seed size For SNP genotyping seed chip method was standardized with technical support from University of Georgia, USA to enhance operational efficiency and optimize resources. 0 10 20 30 40 50 60 2015 2016 2017 100-seedmass(g) ICGV series Average 100-seed mass ::::::::::: Population/plants I I I I I I I Progeny rows SSD = Single Seed Decent SPS = Single Plant Selections BS = Bulk Selections F1Hybridity test by genotyping Elite popular cultivar for a specific trait Recurrent parent (RP) Donor parent (DP) RP BC1F1 RP BC2F1 RP BC3F1BC2F2 BC3F2 Selection based on plan and pod features I I I I I I I I I I I I I I Trials Trials Selection based on genotyping Selection of homozygous plants BC2F3Selection based on plant and pod features BC2F4 BC3F3 Selection based on plant and pod features BC3F4 Progeny bulks Hybridity test by genotyping Rainy 2011 Post-Rainy 2011-12 Rainy 2012 Post-Rainy 2012-13 Rainy 2013 Post-Rainy 2013-14 Rainy 2014 Post-Rainy 2014-15 Rainy 2015 & PR 2015-16 Multi-location evaluation National testing under AICRIP-G Rainy 2016 to 2018 Best lines to be released2019 Phenotyping using NIRS Phenotyping using NIRS Hybridity test by genotyping Hybridity test by genotyping 16 13 32 29 53 28 32 0 5 0 1 26 24 46 56 42 0 10 20 30 40 50 60 70 80 90 0 500 1000 1500 2000 2500 3000 3500 4000 ICGV15105 ICGV15073 ICGV15064 ICGV15052 VRI8 ICGV15106 ICGV15095 ICGV15035 Dharani ICGV15074 ICGV15016 ICGV15006 ICGV15017 GJG9 ICGV15065 ICGV15070 ICGV06420 ICGV15090 ICGV15080 ICGV15083 TG-37A TNAU RARST JAU RARSP DGR Oleicacidcontent(%) Podyield(kg/ha) Pod yield (kg/ha) Oleic acid (%) Figure 2. Performance of 16 high oleic lines under multi-location evaluation trials conducted during rainy 2016. Figures at the top of the bar indicate the percentage increase in pod yield over the best local check Genomics-assisted breeding scheme deployed for introgression of high oleic trait and combining early maturity and resistance to late leaf spot and rust. Table 2. Calibration equations for predicting oil, protein, fatty acids (oleic, linoleic and palmitic acid) and moisture content in whole peanut kernels using NIRS. Constituent N* Mean Range Mathematical treatment RSQ** 1-VR# Oil content (%) 142 48.69 40.08- 57.31 1,4,4,1 0.83 0.80 Protein content (%) 114 27.68 19.73- 35.64 4,6,6,1 0.87 0.75 Palmitic acid (%) 208 11.42 6.77- 16.06 2,4,4,1 0.88 0.80 Oleic acid (%) 208 52.12 23.44- 80.79 2,4,4,1 0.97 0.95 Linoleic acid (%) 208 27.12 2.77- 51.46 2,4,4,1 0.97 0.95 Moisture content (%) 80 10.60 3.70- 23.30 2,4,4,1 0.99 0.99 Promising high oleic line planted for demostration at ICRISAT during rainy 2018. Low-cost controlled greenhouse facility for hybridization and rapid generation advancement (3-4 generations per year).
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