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Genome-wide association and linkage mapping strategies reveal the genetic loci and candidate genes of important agronomic traits in Sichuan wheat
ZHANG Zhi-peng, LI Zhen, HE Fang, LÜ Ji-juan, XIE Bin, YI Xiao-yu, LI Jia-min, LI Jing, SONG Jing-han, PU Zhi-en, MA Jian, PENG Yuan-ying, CHEN Guo-yue, WEI Yu-ming, ZHENG You-liang, LI Wei
2023, 22 (11): 3380-3393.   DOI: 10.1016/j.jia.2023.02.030
Abstract238)      PDF in ScienceDirect      

Increasing wheat yield is a long-term goal for wheat breeders around the world.  Exploiting elite genetic resources and dissecting the genetic basis of important agronomic traits in wheat are the necessary methods for high-yield wheat breeding.  This study evaluated nine crucial agronomic traits found in a natural population of 156 wheat varieties and 77 landraces from Sichuan, China in seven environments over two years.  The results of this investigation of agronomic traits showed that the landraces had more tillers and higher kernel numbers per spike (KNS), while the breeding varieties had higher thousand-kernel weight (TKW) and kernel weight per spike (KWS).  The generalized heritability (H2) values of the nine agronomic traits varied from 0.74 to 0.95.  Structure analysis suggested that the natural population could be divided into three groups using 43 198 single nucleotide polymorphism (SNP) markers from the wheat 55K SNP chip.  A total of 67 quantitative trait loci (QTLs) were identified by the genome-wide association study (GWAS) analysis based on the Q+K method of a mixed linear model.  Three important QTLs were analyzed in this study.  Four haplotypes of QFTN.sicau-7BL.1 for fertile tillers number (FTN), three haplotypes of QKNS.sicau-1AL.2 for KNS, and four haplotypes of QTKW.sicau-3BS.1 for TKW were detected.  FTN-Hap2, KNS-Hap1, and TKW-Hap2 were excellent haplotypes for each QTL based on the yield performance of 42 varieties in regional trials from 2002 to 2013.  The varieties with all three haplotypes showed the highest yield compared to those with either two haplotypes or one haplotype.  In addition, the KASP-AX-108866053 marker of QTL QKNS.sicau-1AL.2 was successfully distinguished between three haplotypes (or alleles) in 63 varieties based on the number of kernels per spike in regional trials between 2018 and 2021.  These genetic loci and reliable makers can be applied in marker-assisted selection or map-based gene cloning for the genetic improvement of wheat yield. 

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Bioinformatic identification and analyses of the non-specific lipid transfer proteins in wheat
FANG Zheng-wu, HE Yi-qin, LIU Yi-ke, JIANG Wen-qiang, SONG Jing-han, WANG Shu-ping, MA Dong-fang, YIN Jun-liang
2020, 19 (5): 1170-1185.   DOI: 10.1016/S2095-3119(19)62776-0
Abstract141)      PDF in ScienceDirect      
Non-specific lipid transfer proteins (nsLTPs/LTPs) that can transport various phospholipids across the membrane in vitro are widespread in the plant kingdom, and they play important roles in many biological processes that are closely related to plant growth and development.  Recently, nsLTPs have been shown to respond to different forms of abiotic stresses.  Despite the vital roles of nsLTPs in many plants, little is known about the nsLTPs in wheat.  In this study, 330 nsLTP proteins were identified in wheat and they clustered into five types (1, 2, c, d, and g) by phylogenetic analysis with the nsLTPs from maize, Arabidopsis, and rice.  The wheat nsLTPs of type d included three subtypes (d1, d2, and d3) and type g included seven subtypes (g1–g7).  Genetic structure and motif pattern analyses showed that members of each type had similar structural composition.  Moreover, GPI-anchors were found to exist in non-g type members from wheat for the first time.  Chromosome mapping revealed that all five types were unevenly and unequally distributed on 21 chromosomes.  Furthermore, gene duplication events contributed to the proliferation of the nsLTP genes.  Large-scale data mining of RNA-seq data covering multiple growth stages and numerous stress treatments showed that the transcript levels of some of the nsLTP genes could be strongly induced by abiotic stresses, including drought and salinity, indicating their potential roles in mediating the responses of the wheat plants to these abiotic stress conditions.  These findings provide comprehensive insights into the nsLTP family members in wheat, and offer candidate nsLTP genes for further studies on their roles in stress resistance and potential for improving wheat breeding programs.
 
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