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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (7): 1016-1024.doi: 10.3724/SP.J.1006.2020.93054

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Fine mapping of a major QTL qMES20-10 associated with deep-seeding tolerance in maize and analysis of differentially expressed genes

REN Meng-Meng1,**,ZHANG Hong-Wei1,**,WANG Jian-Hua2,WANG Guo-Ying1,ZHENG Jun1,*()   

  1. 1 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    2 College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
  • Received:2019-10-12 Accepted:2020-04-15 Online:2020-07-12 Published:2020-04-26
  • Contact: Jun ZHENG E-mail:zhengjun02@caas.cn
  • About author:** Contributed equally to this work
  • Supported by:
    National Key Research and Development Program of China(2016YFD0101002);Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences

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Abstract:

Drought stress is a major threat to maize (Zea mays L.) yield. Deep-seeding tolerant maize variety can absorb water in deep soil and thus have strong drought tolerance. Therefore, it is of great theoretical and practical importance to study the genetic mechanism of deep-seeding tolerance. In our previous work, we identified a major QTL qMES20-10 controlling maize deep-seeding tolerance on chromosome 10 using an F2:3 population derived from a deep-seeding tolerant inbred line 3681-4 and a common inbred line X178. In this study, a BC3F3:4 population was constructed through background and foreground selection using X178 as the recurrent parent. The major QTL, qMES20-10, was firstly verified in this BC3F3:4 population. Furthermore, advanced backcross population was constructed through marker-assisted selection, and qMES20-10 was fine-mapped within the interval of 133.3-136.0 Mb on chromosome 10. Moreover, RNA-Seq analysis of two near-isogenic lines screened from the BC3F3:4 families identified the differentially expressed genes, mainly involved in chemical stimulus response, oxidation reduction, and oxidative stress response. These results lay a foundation of further cloning the major QTL qMES20-10.

Key words: maize, deep-seeding tolerance, QTL, fine mapping, differentially expressed genes

Fig. 1

Phenotyping method and phenotype of the two parents A: diagram of phenotyping method. B: mesocotyl of two parents sowing in 20 cm roseite, scale bar = 1 cm. C: mesocotyl length of two parents; ** means significant difference at P < 0.01."

Table 1

Primers used in this study"

引物
Primer		 物理位置
Position		 正向序列
Forward sequence (5'-3')		 反向序列
Reverse sequence (5'-3')
umc1506 133,239,898 ATAAAGGTTGGCAAAACGTAGCCT AAAAGAAACATGTTCAGTCGAGCG
DST_InD25 133,799,178 TGCGCTTTATTAGGCGAAAC TTTACGCGTTATGGGAGACC
DST_Ind7 134,830,243 GCTTGCTGCATTGTCTTGAA GGCAGATTGACACTGGTGAA
DST_Ind105 136,072,789 AGAGAGACAGCCGCACTTG TCGACCGTACTTGTTCATGG
DST_InD13 136,274,298 GGCAACAGTTCGACGGATTA TCCGGATGATGTTTACATGG
bnlg1028 138,503,281 AGGAAACGAACACAGCAGCT TGCATAGACAAAACCGACGT

Fig. 2

Validation of the major QTL qMES20-10 for deep-seeding tolerance A: mesocotyl length of seedlings in three different genotypes of BC3F3:4 lines. A, H, B denote homozygous X178, heterozygous, and homozygous 3681-4 genotype respectively. P-value is determined by ANOVA for mesocotyl length of different genotypic seedlings. B: QTL-mapping using BC3F3:4 lines in the whole genome."

Fig. 3

Fine mapping of the major QTL qMES20-10 for deep-seeding tolerance A: the locus of target QTL qMES20-1 on bin 10.06. B: fine-mapping utilizing BC4F2:3 lines. R1-R9 represent the nine recombinant types. Black and white bars represent chromosomal segments derived from 3681-4 and X178. ** and * mean significant difference at the P < 0.01 and P < 0.05, respectively; NS means no significant difference."

Fig. 4

Validation of the mapping region using progeny test A: the crossover regions of the recombinants. B: progeny test of the recombinants. Black, white, and grey bars represent homozygous regions for 3681-4, homozygous regions for X178 and heterozygous regions, respectively. n means the number of plants with different genotype; P-values were determined by Student’s t test for mesocotyl length of plants with different genotype."

Fig. 5

Statistics and distribution of differentially expressed genes A: Venn diagram of differentially expressed genes. B: distribution of differentially expressed genes on chromosomes. The big and small circles denote differentially expressed genes of two parents and NILs respectively. P-value is determined by students’ t-test, and red dots represent genes with P-value < 0.0001."

Fig. 6

GO analysis of differentially expressed genes in near-isogenic lines A: grey boxes show the GO terms that can be enriched. B: enriched differentially expressed genes related to plant hormone signal transduction according to KEGG."

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