Marker Assisted Development of Region-Specific In Vivo Haploid Inducers to Enhance Maize Breeding in Northeast India

Abstract

Hybrid breeding of maize depends on the rapid development of pure inbred lines. Doubled haploid technology utilizing the mtl (matrilineal) gene from Stock6 accelerates the process to a great extent. Although temperate haploid inducer lines exhibit high haploid induction rates, they are not well adapted to the varied agro-ecological environments of India, especially in the Northeast (NE). To develop region-specific Haploid Inducer (HI) lines, marker assisted selection was employed by crossing local inbred maize lines (as females) with the HI line EC9044833, which served as the mtl gene donor, and R1-nj dominant anthocyanin colour marker for haploid seed identification. Genotyping results confirmed polymorphism between the wild-type and mutant mtl alleles with F₂ populations exhibiting significant segregation distortion. The R1-nj marker showed stable inheritance, though its penetrance varied among sibling cobs in advanced generations. Selection for high penetrance and homozygosity at the mtl locus enabled the enrichment of putative HI lines with strong marker expression. Across two seasons, haploid induction rate (HIR) ranged from 0.4% to 14% among F₄ and F₅ families, with high genetic variance and selection accuracy (0.88), leading to a substantial 47% genetic gain in HIR from F₄ to F₅ generations. Promising HI families, particularly C1-7 and D-18 with HIR ≥ 6%, were selected and would be further evaluated for agronomic and tassel traits to enhance overall inducer performance. This study demonstrates the successful initiation for developing a robust, high-performing inducers suited to local agro-climatic conditions of NE India.