Abstract
BackgroundResidual heterozygosity (RH) in advanced inbred lines of plants benefits quantitative trait locus (QTL) mapping studies. However, knowledge of factors affecting the genome-wide distribution of RH remains limited.ResultsA set of 2196 heterogeneous inbred family (HIF) maize lines derived from 12 recombinant inbred line (RIL) populations was genotyped using the Maize50K SNP chip. A total of 18,615 unique RH intervals were identified, ranging from 505 to 2095 intervals per population, with average maize genome coverage of 94.8%. Across all populations, there were 8.6 RH intervals per HIF line on average, ranging from 1.8 to 14 intervals; the average size of an RH interval was approximately 58.7 Mb, ranging from 7.2 to 74.1 Mb. A given RH region was present in an average of 5 different individuals within a population. Seven RH hotspots, where RH segments were enriched in the genome, were found to be subject to selection during population development. The RH patterns varied significantly across populations, presumably reflecting differences in the genetic background of each population, and 8 QTLs were found to affect heterozygosity levels in the RH hotspots. The potential use of this HIF library for the fine mapping of QTLs was assessed based on publicly available QTL information, achieving a ≤ 1 Mb resolution on average.ConclusionThe examined library of HIF lines offers insight into the RH landscape and its intraspecific variation and provides a useful resource for the QTL cloning of important agronomic traits in maize.
Highlights
Residual heterozygosity (RH) in advanced inbred lines of plants benefits quantitative trait locus (QTL) mapping studies
10 RH intervals per line were observed in the F6 populations and 4 in the recombinant inbred line (RIL) and backcross populations, with average lengths of 6.7 and 4.1 Mb per interval, respectively (Table 1)
To explore the mechanisms underlying the relationship between RH hotspots and heterosis, we evaluated the frequencies of two alleles and recombination rates within 2 Mb on each side of the RH hotspots
Summary
Residual heterozygosity (RH) in advanced inbred lines of plants benefits quantitative trait locus (QTL) mapping studies. The identification of genes underlying traits of agricultural and economic importance is a long-term objective that will enhance the understanding of the architecture of complex traits and accelerate crop genetic improvement To this end, two methods have been routinely used in plants. The gene-driven reverse genetics approach, based on the availability of large mutagenized libraries, has been employed to explore phenotypes associated with a specific mutated gene variant. In maize, tools such as transposons, T-DNA, ethyl methane sulfonate (EMS) mutagenesis, and genome editing have been commonly used to develop mutant libraries [8]. The HIF approach has been successfully applied to QTL cloning for many important traits related to plant morphology, diseases, flowering time, and seed weight in several species [13,14,15]
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