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Single Seed-Based High-Throughput Genotyping and Rapid Generation Advancement for Accelerated Groundnut Genetics and Breeding Research

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Relation http://oar.icrisat.org/11876/
https://doi.org/10.3390/agronomy11061226
doi:10.3390/agronomy11061226
 
Title Single Seed-Based High-Throughput Genotyping and Rapid Generation Advancement for Accelerated Groundnut Genetics and Breeding Research
 
Creator Parmar, S
Deshmukh, D B
Kumar, R
Manohar, S S
Joshi, P
Sharma, V
Chaudhari, S
Variath, M T
Gangurde, S S
Bohar, R
Singam, P
Varshney, R K
Janila, P
Pandey, M K
 
Subject Plant Breeding
Groundnut
Genetics and Genomics
 
Description The groundnut breeding program at International Crops Research Institute for the Semi-
Arid Tropics routinely performs marker-based early generation selection (MEGS) in thousands of
segregating populations. The existing MEGS includes planting of segregating populations in fields
or glasshouses, label tagging, and sample collection using leaf-punch from 20–25 day old plants
followed by genotyping with 10 single nucleotide polymorphisms based early generation selection
marker panels in a high throughput genotyping (HTPG) platform. The entire process is laborious,
time consuming, and costly. Therefore, in order to save the time of the breeder and to reduce the
cost during MEGS, we optimized a single seed chipping (SSC) process based MEGS protocol and
deployed on large scale by genotyping >3000 samples from ongoing groundnut breeding program. In
SSC-based MEGS, we used a small portion of cotyledon by slicing-off the posterior end of the single
seed and transferred to the 96-deep well plate for DNA isolation and genotyping at HTPG platform.
The chipped seeds were placed in 96-well seed-box in the same order of 96-well DNA sampling
plate to enable tracking back to the selected individual seed. A high germination rate of 95–99%
from the chipped seeds indicated that slicing of seeds from posterior end does not significantly
affect germination percentage. In addition, we could successfully advance 3.5 generations in a year
using a low-cost rapid generation turnover glass-house facility as compared to routine practice of
two generations in field conditions. The integration of SSC based genotyping and rapid generation
advancement (RGA) could significantly reduce the operational requirement of person-hours and
expenses, and save a period of 6–8 months in groundnut genetics and breeding research.
 
Publisher MDPI
 
Date 2021-06
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Identifier http://oar.icrisat.org/11876/1/agronomy-11-01226.pdf
Parmar, S and Deshmukh, D B and Kumar, R and Manohar, S S and Joshi, P and Sharma, V and Chaudhari, S and Variath, M T and Gangurde, S S and Bohar, R and Singam, P and Varshney, R K and Janila, P and Pandey, M K (2021) Single Seed-Based High-Throughput Genotyping and Rapid Generation Advancement for Accelerated Groundnut Genetics and Breeding Research. Agronomy (TSI), 11 (6). pp. 1-15. ISSN 2073-4395