Development and validation of gene‐based markers for shrunken2‐Reference allele and their utilization in marker‐assisted sweet corn (Zea maysSachharata) breeding programme

Abstract

The recessive shrunken2-Reference (sh2-Ref) allele is traditionally used in sweet corn cultivar development worldwide. However, non-availability of suitable gene-based marker(s) for sh2-Ref has considerably delayed its utilization in molecular breeding. Here, 7,320 bp sequence of Sh2 gene among five wild-and six sh2-Ref-based inbreds was analysed by employing 13 overlapping primers. SNP583 (A in wild and G in mutant) and SNP755 (T in wild and C in mutant) in 5'UTR, and SNP5112 (C in wild and T in mutant) in intron-12 clearly differentiated dominant (Sh2) and recessive (sh2-Ref) allele. These SNPs were used to develop four gene-based PCR markers. The newly developed markers were validated in six F 2 populations segregating for sh2-Ref allele, and 230 diverse inbreds of normal and sweet corn types. These markers were further used in genotyping of BC 1 F 1 populations leading to successful selection of sh2-Ref allele in the marker-assisted breeding. Globally, this assumes great significance in molecular breeding of sweet corn.

Identification of Gene Associated with Sweetness in Corn (Zea mays L.) by Genome-Wide Association Study (GWAS) and Development of a Functional SNP Marker for Predicting Sweet Corn

“…Among these, six SNPs had a missense effect, two SNPs were located on the introns, and two SNPs were located upstream the first start codon ( Figure 4 ). These SNPs are different from those used to develop the gene-based markers for sh2-Reference allele [ 15 ]. The markers were designed on the basis of these 10 selected SNPs and validated in a set of 43 maize lines using a MassARRAY ® platform ( Table S4 ).…”

“…However, there is no report of functional markers associated with genes or QTLs underlying kernel sweetness in maize. Chhabra et al (2020) recently reported gene-based PCR markers that resided in the 5’UTR and intron-12 regions of the sh2 gene [ 15 ]. In this study, we extended the search for gene-based SNPs around our most associated SNP near the sh2 gene on chromosome 3.…”

“…However, functional markers for selecting the sweetness trait in maize are still limited in the public sector and some private companies. Recently, gene-based markers for shunken2-Reference allele have been developed and used in marker-assisted sweet corn ( Zea mays Sachharata ) breeding program [ 15 ].…”

Allelic variation in shrunken2 gene affecting kernel sweetness in exotic-and indigenous-maize inbreds

“…US$ 1541.72 million and US$ 1475 million worth of import and export were recorded in sweet corn during 2020, respectively [ 7 ]. The kernel sweetness is genetically controlled, thus identification of mutations in gene(s) involved in the starch biosynthesis pathway provides gateway to enhance sweetness in kernels [ 8 , 9 ]. Amongst various mutations reported till date, a recessive shrunken2 ( sh2 ) gene located on chromosome 3L at bin location 3.09, has been widely used in the sweet corn breeding programmes [ 10 ].…”

“…Recessive sh2 mutation was first identified as loss of function gene [ 11 ] and it was later artificially selected by the breeders to develop sweet corn germplasm globally [ 12 , 13 ]. Using this sh2 mutant, large number of sh2 -based sweet corn inbreds and hybrids has been developed and commercialized [ 8 , 14 ]. Sh2 gene encodes the large subunit of ADP-glucose pyrophosphorylase ( AGPase ) that catalyzes the conversion of glucose-1-phosphate into ADP-glucose in the starch biosynthesis pathway [ 15 ].…”