Haplotypes of recessive opaque2 allele in exotic- and indigenous-quality protein maize inbreds

NEHA PANDEY; FIROZ HOSSAIN; VIGNESH MUTHUSAMY; ASHISH K VISHWAKARMA; RAJKUMAR U ZUNJARE

doi:10.56093/ijas.v88i2.79199

Authors

NEHA PANDEY ICAR-Indian Agricultural Research Institute, New Delhi 110 012
FIROZ HOSSAIN Senior Scientist (Maize Gentics and Breeding), ICAR-Indian Agricultural Research Institute, New Delhi 110 012
VIGNESH MUTHUSAMY ICAR-Indian Agricultural Research Institute, New Delhi 110 012
ASHISH K VISHWAKARMA ICAR-Indian Agricultural Research Institute, New Delhi 110 012
RAJKUMAR U ZUNJARE ICAR-Indian Agricultural Research Institute, New Delhi 110 012

https://doi.org/10.56093/ijas.v88i2.79199

Keywords:

Cluster analyses, Exon, Haplotype, Opaque2, QPM, SSR

Abstract

Forty six QPM inbreds of diverse origin were genotyped using opaque2 (o2)-specific SSRs viz. umc1066 and phi057, present on exon-1 and exon-6 of the gene, respectively. These SSRs are the polymorphic sites that differentiate dominant (O2) and recessive (o2) alleles. A total of two alleles (o2-A and o2-B) of umc1066, and three alleles (o2-C, o2-D and o2-E) of phi057 were identified. o2-A allele (93.48%) was the most abundant, while o2-B allele was observed only in 6.52% of the inbreds. For phi057 locus, o2-E allele had the highest frequency (80.17%), followed by o2-D (19.57%) and o2-C (2.17%). Among various haplotypes, o2-AE had the highest frequency (76.09%), followed by o2-AD (15.22%) and o2-BD (4.35%). o2-BC and o2-AC haplotypes were observed in 2.17% each of the inbreds. Haplotype, o2-BE was not found in the inbred panel. Cluster analyses grouped the inbreds into two major clusters with inbreds being together based on haplotypes. All the inbreds developed at PJTSAU, Hyderabad, CSK HPKV, Bajaura, and CCS HAU, Uchani and majority of inbreds from CIMMYT, Mexico had the o2-AE haplotype. Inbreds developed at VPKAS, Almora had three haplotypes viz. o2-BC, o2-AD and o2-AE. Inbreds from IARI, New Delhi had o2-AE and o2-AD haplotypes, while inbreds developed at IIMR, New Delhi had o2-AE and o2-AC haplotypes. o2-BD was identified as the most promising haplotype for accumulation of lysine and tryptophan in the endosperm, followed by o2-AE. o2-BC haplotype was the least promising for nutritional quality. o2-AC, o2-AD and o2-BC possessed 25% opaqueness, while o2-BD had 50% opaqueness. Broad range of 25-100% opaqueness was observed among inbreds possessing o2-AE haplotype. So far, breeders perceive that only one recessive o2 allele exist in the population, and any QPM inbred serves as a donor of the o2 allele in the QPM breeding programme. The present study reports here the occurrence of at least five versions of recessive o2 allele, and the information generated here can benefit the QPM breeding programme by selectively introgressing the most favourable haplotype allele of o2 over other haplotypes.

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