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Journal of Integrative Agriculture  2020, Vol. 19 Issue (6): 1543-1553    DOI: 10.1016/S2095-3119(19)62683-3
Special Issue: 麦类遗传育种合辑Triticeae Crops Genetics · Breeding · Germplasm Resources
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dCAPS markers developed for nitrate transporter genes TaNRT2L12s associating with 1 000-grain weight in wheat
HUANG Jun-fang1, 2, LI Long2, MAO Xin-guo2, WANG Jing-yi2, LIU Hui-min1, LI Chao-nan2, JING Rui-lian2 
1 College of Bioengineering, Shanxi University, Taiyuan 030006, P.R.China
2 National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
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Nitrate transporters (NRTs) are regulators of nitrate assimilation and transport.  The genome sequences of TaNRT2L12-A, -B and -D were cloned from wheat (Triticum aestivum L.), and polymorphisms were analyzed by sequencing.  TaNRT2L12-D in a germplasm population was highly conserved.  However, 38 single nucleotide polymorphisms (SNPs) in TaNRT2L12-A coding region and 11 SNPs in TaNRT2L12-B coding region were detected.  Two derived cleaved amplified polymorphic sequences (dCAPS) markers A-CSNP1 and A-CSNP2 were developed for TaNRT2L12-A based on SNP-351 and SNP-729, and three haplotypes were identified in the germplasm population.  B-CSNP1 and B-CSNP2 were developed for TaNRT2L12-B based on SNP-237 and SNP-1 227, and three haplotypes were detected in the germplasm population.  Association analyses between the markers and agronomic traits in 30 environments and phenotypic comparisons revealed that A-CSNP2-A is a superior allele of shorter plant height (PH), length of penultimate internode (LPI) and peduncle length (PL), B-CSNP2-G is a superior allele of higher grain number per spike (GNS).  Hap-6B-1 containing both superior alleles B-CSNP1-C and B-CSNP2-A is a superior haplotype of 1 000-grain weight (TGW).  Expression analysis showed that TaNRT2L12-B is mainly expressed in the root base and regulated by nitrate.  Therefore, TaNRT2L12 may be involved in nitrate transport and signaling to regulate TGW in wheat.  The superior alleles and dCAPS markers of TaNRT2L12-A/B are beneficial to genetic improvement and germplasm enhancement with molecular markers-assisted selection. 
Keywords:  Triticum aestivum L.        TaNRT2L12        association analysis        single nucleotide polymorphism        dCAPS marker        haplotypes  
Received: 18 February 2019   Accepted:
Fund: This work was supported by the National Key Research and Development Program of China (2017YFD0300202) and the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences (ASTIP).
Corresponding Authors:  Correspondence LI Chao-nan, Tel: +86-10-82105829, E-mail:; JING Rui-lian, Tel: +86-10-82105829, E-mail:   

Cite this article: 

HUANG Jun-fang, LI Long, MAO Xin-guo, WANG Jing-yi, LIU Hui-min, LI Chao-nan, JING Rui-lian. 2020. dCAPS markers developed for nitrate transporter genes TaNRT2L12s associating with 1 000-grain weight in wheat. Journal of Integrative Agriculture, 19(6): 1543-1553.

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