QTL Mapping Low-Temperature Germination Ability in the Maize IBM Syn10 DH Population

Abstract

Chilling injury poses a serious threat to seed emergence of spring-sowing maize in China, which has become one of the main climatic limiting factors affecting maize production in China. It is of great significance to mine the key genes controlling low-temperature tolerance during seed germination and study their functions for breeding new maize varieties with strong low-temperature tolerance during germination. In this study, 176 lines of the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, which comprised 6618 bin markers, were used for QTL analysis of low-temperature germination ability. The results showed significant differences in germination related traits under optimum-temperature condition (25 °C) and low-temperature condition (10 °C) between two parental lines. In total, 13 QTLs were detected on all chromosomes, except for chromosome 5, 7, 10. Among them, seven QTLs formed five QTL clusters on chromosomes 1, 2, 3, 4, and 9 under the low-temperature condition, which suggested that there may be some genes regulating multiple germination traits at the same time. A total of 39 candidate genes were extracted from five QTL clusters based on the maize GDB under the low-temperature condition. To further screen candidate genes controlling low-temperature germination, RNA-Seq, in which RNA was extracted from the germination seeds of B73 and Mo17 at 10 °C, was conducted, and three B73 upregulated genes and five Mo17 upregulated genes were found by combined analysis of RNA-Seq and QTL located genes. Additionally, the variations of Zm00001d027976 (GLABRA2), Zm00001d007311 (bHLH transcription factor), and Zm00001d053703 (bZIP transcription factor) were found by comparison of amino sequence between B73 and Mo17. This study will provide a theoretical basis for marker-assisted breeding and lay a foundation for further revealing molecular mechanism of low-temperature germination tolerance in maize.

Transcriptome Analysis of Near-Isogenic Lines Provides Novel Insights into Genes Associated with Seed Low-Temperature Germination Ability in Maize (Zea mays L.)

“…In general, seed germination speed reduces when germination temperature decreases. For maize, it was reported that the minimum temperature for germination is 10 °C [ 33 ], and it was commonly set as 10 °C for the low temperature germination treatment [ 31 , 34 , 35 ]. We previously used this experimental condition to conduct QTL mapping in an F 2:3 population crossed from L220 and PH4CV and identify a major QTL, qp1ER1-1, for maize LTGA [ 31 ].…”

“…Seed harvested from L220, PH4CV, and NILs were used for LTGA evaluation according to the methods described by Li et al (2018) and Zhang et al (2020) [ 31 , 35 ]. For emergence rate testing, 30 seeds were surface sterilized for 5 min in 0.1% sodium hypochlorite and rinsed three times with distilled water, then sown in sterile sand with moisture content of 16% in a plastic box, which incubated in a dark chamber at 10 °C ER was defined as shoots breaking through the sand and counted from 17 to 25 days after sowing (DAS) with a 2-day interval.…”

RAD-Seq-Based High-Density Linkage Maps Construction and Quantitative Trait Loci Mapping of Flowering Time Trait in Alfalfa (Medicago sativa L.)

“…Previous studies into FT mainly focused on QTL mapping in alfalfa (in genomics level) ( Adhikari et al, 2019 ; Zhang et al, 2020 ). Although integration of QTL mapping and RNA-seq has been applied to identify candidate genes in rice, maize ( Zea mays L.), wheat ( Triticum aestivum L.), and other crops ( Kuang et al, 2020 ; Lei et al, 2020 ; Han et al, 2022 ), but such approaches have not been used for discovering alfalfa FT genes. In this study, flower samples at three flowering stages from two parents of the F 1 mapping population were characterized using the RNA-seq technology, and the identified DEGs were combined with QTLs to narrow the candidates.…”

Recent developments in multi-omics and breeding strategies for abiotic stress tolerance in maize (Zea mays L.)

“…The genes with putative function related to auxin and gibberellin response were identified in the QTL region. Recently, Han et al (2022) mapped five QTL clusters on chromosomes 1, 2, 3, 4, and 9 using an B73 x Mo17 (IBM) Syn10 double haploid population. From these clusters, 39 genes were extracted, and through RNA-seq, upregulated genes from B73 and Mo17 were identified.…”