Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize

Zhang, Yinchao; Liu, Peng; Wang, Chen; Zhang, Na; Zhu, Yuxiao; Zou, Chaoying; Yang, Cong; Pan, Guangtang; Ma, Langlang; Shen, Yaou

doi:10.7717/peerj.11707

Cited by 22 publications

(17 citation statements)

References 52 publications

(60 reference statements)

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“…GWAS was performed using the rMVP package in R ( Yin et al, 2021 ). Based on the observation of p -values in different models under quantile–quantile (Q–Q) plots, the FarmCPU was selected as the most suitable model ( Kaler et al, 2017 ; Zhang et al, 2021 ). The Bonferroni of false discovery rate (FDR) correction of 5% calculated by the rMVP package was used for multiple comparison adjustment and as a threshold to identify significant marker-trait associations ( Aguado et al, 2020 ; Megerssa et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

Screening of stable resistant accessions and identification of resistance loci to Barley yellow mosaic virus disease

Pan

Jun

Hong

et al. 2022

PeerJ

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Background The disease caused by Barley yellow mosaic virus (BaYMV) infection is a serious threat to autumn-sown barley (Hordeum vulgare L.) production in Europe, East Asia and Iran. Due to the rapid diversification of BaYMV strains, it is urgent to discover novel germplasm and genes to assist breeding new varieties with resistance to different BaYMV strains, thus minimizing the effect of BaYMV disease on barley cropping. Methods A natural population consisting of 181 barley accessions with different levels of resistance to BaYMV disease was selected for field resistance identification in two separate locations (Yangzhou and Yancheng, Jiangsu Province, China). Additive main effects and multiplicative interaction (AMMI) analysis was used to identify accessions with stable resistance. Genome-wide association study (GWAS) of BaYMV disease resistance was broadly performed by combining both single nucleotide polymorphisms (SNPs) and specific molecular markers associated with the reported BaYMV disease resistance genes. Furthermore, the viral protein genome linked (VPg) sequences of the virus were amplified and analyzed to assess the differences between the BaYMV strains sourced from the different experimental sites. Results Seven barley accessions with lower standardized Area Under the Disease Progress Steps (sAUDPS) index in every environment were identified and shown to have stable resistance to BaYMV disease in each assessed location. Apart from the reported BaYMV disease resistance genes rym4 and rym5, one novel resistance locus explaining 24.21% of the phenotypic variation was identified at the Yangzhou testing site, while two other novel resistance loci that contributed 19.23% and 19.79% of the phenotypic variation were identified at the Yancheng testing site, respectively. Further analysis regarding the difference in the VPg sequence of the predominant strain of BaYMV collected from these two testing sites may explain the difference of resistance loci differentially identified under geographically distinct regions. Our research provides novel genetic resources and resistance loci for breeding barley varieties for BaMYV disease resistance.

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Section: Methodsmentioning

confidence: 99%

Screening of stable resistant accessions and identification of resistance loci to Barley yellow mosaic virus disease

Pan

Jun

Hong

et al. 2022

PeerJ

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“…Fourteen candidate genes directly related to the SNPs were found and further verified by gene expression analysis. Zhang et al ( 2021 ) studied germination-related traits in 300 inbred lines under low temperature conditions. GWAS analysis revealed a total of 15 significant SNPs, and three genomic loci were repeatedly associated with multiple traits.…”

Section: Genetic and Genomic Approaches To Dissect Cold Tolerance In ...mentioning

confidence: 99%

Recent Advances in the Analysis of Cold Tolerance in Maize

Zhou

Imran²,

Long

et al. 2022

Front. Plant Sci.

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Maize (Zea mays L.) is an annual grass that originated in tropical and subtropical regions of the New World. Maize is highly sensitive to cold stress during seed gemination and the seedling phase, which can lead to reductions in plant vigor and grain production. There are large differences in the morphological and physiological changes caused by cold stress among maize varieties. In general, cold tolerant varieties have a stronger ability to maintain such changes in traits related to seed germination, root phenotypes, and shoot photosynthesis. These morphological and physiological characteristics have been widely used to evaluate the cold tolerance of maize varieties in genetic analyses. In recent years, considerable progress has been made in elucidating the mechanisms of maize in response to cold tolerance. Several QTL, GWAS, and transcriptomic analyses have been conducted on various maize genotypes and populations that show large variations in cold tolerance, resulting in the discovery of hundreds of candidate cold regulation genes. Nevertheless, only a few candidate genes have been functionally characterized. In the present review, we summarize recent progress in molecular, physiological, genetic, and genomic analyses of cold tolerance in maize. We address the advantages of joint analyses that combine multiple genetic and genomic approaches to improve the accuracy of identifying cold regulated genes that can be further used in molecular breeding. We also discuss the involvement of long-distance signaling in plant cold tolerance. These novel insights will provide a better mechanistic understanding of cold tolerance in maize.

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“…The germination and growth of maize, which was originated from tropical and subtropical areas, were seriously threatened by chilling injury in early spring. Under low temperature, germination rate was decreased in maize, while the elongation of plumule length, seedling length, and root length were inhibited [1]. The low seed vigor and poor low-temperature tolerance of cultivated varieties had led to irregular emergence and seedling absent in early spring.…”

Section: Introductionmentioning

confidence: 99%

“…Different from excessive reports at the maize seedling stage, there were few associated analyses related to low-temperature germination ability. Combining 43,943 SNPs, 15 significant SNPs, including three overlapped loci, were associated with germination rate, root length, and shoot length of 300 inbred lines by GWAS under cold stress [1]. In our previous study, 15 QTLs, located on chromosomes 4, 5, 6, 7, and 9, regulating low-temperature germination ability were mapped by 243 Syn4 recombinant inbred line (RIL) populations, which were derived from B73 and Mo17 [15].…”

Section: Introductionmentioning

confidence: 99%

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

Han

Zhu

Shen

et al. 2022

Plants

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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.

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Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize

Cited by 22 publications

References 52 publications

Screening of stable resistant accessions and identification of resistance loci to Barley yellow mosaic virus disease

Screening of stable resistant accessions and identification of resistance loci to Barley yellow mosaic virus disease

Recent Advances in the Analysis of Cold Tolerance in Maize

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

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