QTL mapping of spontaneous haploid genome doubling using genotyping-by-sequencing in maize (Zea mays L.)

Abstract

Genome doubling of haploids is one of the major constraints of large-scale doubled haploid (DH) technology. Improving spontaneous haploid genome doubling (SHGD) is an alternative to overcome this limitation. In this study, we aimed to construct a high-density linkage map based on genotyping by sequencing (GBS) of Single Nucleotide Polymorphism (SNPs), to detect QTL and QTL by environment (Q by E) interactions affecting SHGD, and to identify the best trait for mapping and selection of haploid male fertility (HMF). To this end, a bi-parental population of 220 F2:3 families was developed from a cross between A427 (high HMF) and CR1Ht (moderate HMF) to be used as donor. A high-density linkage map was constructed containing 4,171 SNP markers distributed over 10 chromosomes with an average distance between adjacent markers of 0.51 cM. QTL mapping for haploid fertile anther emergence (AE), pollen production (PP), tassel size (TS), and HMF, identified 27 QTL across three environments, and Q by E interactions were significant. A major QTL was identified on chromosome 5. This QTL explained over 45% of the observed variance for all traits across all environments. The introgression of this major QTL, using marker-assisted backcrossing, has great potential to overcome the need of using colchicine in DH line development.

Impact of Spontaneous Haploid Genome Doubling in Maize Breeding

“…Recently, five inbred lines exhibiting haploid male fertility (HMF) greater than 65% without the use of colchicine were identified by their pollen-shedding ability and proportion of anther emergence [20]. Furthermore, a single large-effect QTL has been identified on chromosome 5 in the inbred that had the highest level of HMF, at 94% [21,22]. Interestingly, this QTL is different from that identified on chromosome 6 within an inbred developed in China that also possesses a high degree of HMF [23].…”

“…Possible candidate genes for large-effect SHGD QTL have been suggested [21,23]. The gene absence of first division (afd1) is characterized by having an absence of first division during meiosis Furthermore, linkage mapping within a bi-parental mapping population using the same high SHGD parent as was used by Ren et al [21] identified a large-effect QTL possessing additive gene action in the same region as qshgd1 ( Figure 2) [22]. Similarly, two small-effect QTL in the same regions as qshgd2 and qshgd3 identified by Ren et al [21] were also detected ( Figure 2) [22].…”

“…The gene absence of first division (afd1) is characterized by having an absence of first division during meiosis Furthermore, linkage mapping within a bi-parental mapping population using the same high SHGD parent as was used by Ren et al [21] identified a large-effect QTL possessing additive gene action in the same region as qshgd1 ( Figure 2) [22]. Similarly, two small-effect QTL in the same regions as qshgd2 and qshgd3 identified by Ren et al [21] were also detected ( Figure 2) [22]. These differing QTL between the Chinese and US germplasms indicate that there are likely multiple mechanisms underlying similar phenotypes, possibly depending on the origin of germplasm.…”

“…Due to the genetic diversity of SHGD donors in the abovementioned mapping studies, and the quantitative nature of most alleles, introgression of SHGD into a breeding program could be quite challenging. At least four QTL on chromosomes 3, 5, 6, and 10 have been identified by QTL mapping studies [21][22][23]38] and may be useful to increase SHGD ability in elite germplasm. The single large-effect locus on chromosome 5 identified by Ren et al and Trampe et al [21,22] should simplify introgression into elite germplasm by established MABC procedures.…”

“…Multiple approaches for introgression can be taken, depending on the desired level of recurrent parent genome (RPG) to be recovered and number of genes or QTL controlling the chosen mechanism of SHGD. Inheritance of SHGD is mediated both by single large-effect QTL [21][22][23] and multiple small-effect QTL [19,33,34,38]. The methods used to introgress SHGD into elite germplasm depend on the SHGD source and its underlying genetic mechanism.…”