Genome-wide association study to identify genomic regions influencing spontaneous fertility in maize haploids

Vijay Chaikam,Albrecht E Melchinger,Prasanna M Boddupalli,Sudha K Nair,Manje Gowda

doi:10.1007/s10681-019-2459-5

Vijay Chaikam, Albrecht E Melchinger + Show 3 more

Open Access

https://doi.org/10.1007/s10681-019-2459-5

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Abstract

Efficient production and use of doubled haploid lines can greatly accelerate genetic gains in maize breeding programs. One of the critical steps in standard doubled haploid line production is doubling the haploid genome using toxic and costly mitosis-inhibiting chemicals to achieve fertility in haploids. Alternatively, fertility may be spontaneously restored by natural chromosomal doubling, although generally at a rate too low for practical applications in most germplasm. This is the first large-scale genome-wise association study to analyze spontaneous chromosome doubling in haploids derived from tropical maize inbred lines. Induction crosses between tropicalized haploid inducers and 400 inbred lines were made, and the resulting haploid plants were assessed for haploid male fertility which refers to pollen production and haploid fertility which refers to seed production upon self-fertilization. A small number of genotypes were highly fertile and these fertility traits were highly heritable. Agronomic traits like plant height, ear height and tassel branch number were positively correlated with fertility traits. In contrast, haploid induction rate of the source germplasm and plant aspect were not correlated to fertility traits. Several genomic regions and candidate genes were identified that may control spontaneous fertility restoration. Overall, the study revealed the presence of large variation for both haploid male fertility and haploid fertility which can be potentially exploited for improving the efficiency of doubled haploid derivation in tropical maize germplasm.

Highlights

Haploids have become very important in maize breeding as a source of completely homozygous inbred lines, referred to as doubled haploid (DH) lines
Haploid male fertility (HMF) and Haploid fertility (HF) data were transformed by applying a logit-transformation
ANOVA revealed significant genotypic and genotype x environment interactions (GxE) variances for HMF, whereas only genotypic variances were significant for HF

Summary

Introduction

Haploids have become very important in maize breeding as a source of completely homozygous inbred lines, referred to as doubled haploid (DH) lines. Haploids are generated in vivo in maize by pollinating the source germplasm with pollen from maternal haploid inducers (Chaikam 2012). The resulting seeds/seedlings are sorted based on various markers (Chaikam et al 2016; Chase and Nanda 1965; Melchinger et al 2014), and the selected haploid seed (D0 seed) is generally used in DH production. Due to misclassification or inhibition of markers used for classification of induction cross seed, the resulting D0 seed usually includes false positive (hybrid) seed, which are later removed in the DH nursery based on their phenotype (Mahuku 2012; Prigge and Melchinger 2012). DH lines are produced by self-pollinating the fertile haploid plants (Chaikam and Mahuku 2012; Prigge and Melchinger 2012)

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