Genome wide association analysis for yield related traits in maize.

BACKGROUND: Understanding the genetic basis of yield related traits contributes to the improvement of grain yield in maize. RESULTS: Using 291 excellent maize inbred lines as materials, six yield related traits of maize, including grain yield per plant (GYP), grain length (GL), grain width (GW), kernel number per row (KNR), 100 kernel weight (HKW) and tassel branch number (TBN) were investigated in Jinan, in 2017, 2018 and 2019. The average values of three environments were taken as the phenotypic data of yield related traits, and they were statistically analyzed. Based on 38,683 high-quality SNP markers in the whole genome of the association panel, the MLM with PCA model was used for genome-wide association analysis (GWAS) to obtain 59 significantly associated SNP sites. Moreover, 59 significantly associated SNPs (P < 0.0001) referring to GYP, GL, GW, KNR, HKW and TBN, of which 14 SNPs located in yield related QTLs/QTNs previously reported. A total of 66 candidate genes were identified based on the 59 significantly associated SNPs, of which 58 had functional annotation. CONCLUSIONS: Using genome-wide association analysis strategy to identify genetic loci related to maize yield, a total of 59 significantly associated SNP were detected. Those results aid in our understanding of the genetic architecture of maize yield and provide useful SNPs for genetic improvement of maize.

Functional analysis revealed the involvement of ZmABCB15 in resistance to rice black-streaked dwarf virus infection.

BACKGROUND: Maize rough dwarf disease (MRDD), caused by rice black-streaked dwarf virus (RBSDV) belonging to the Fijivirus genus, seriously threatens maize production worldwide. Three susceptible varieties (Ye478, Zheng 58, and Zhengdan 958) and two resistant varieties (P138 and Chang7-2) were used in our study. RESULTS: A set of ATP-binding cassette subfamily B (ABCB) transporter genes were screened to evaluate their possible involvements in RBSDV resistance. In the present study, ZmABCB15, an ABCB transporter family member, was cloned and functionally identified. Expression analysis showed that ZmABCB15 was significantly induced in the resistant varieties, not in the susceptible varieties, suggesting its involvement in resistance to the RBSDV infection. ZmABCB15 gene encodes a putative polar auxin transporter containing two trans-membrane domains and two P-loop nucleotide-binding domains. Transient expression analysis indicated that ZmABCB15 is a cell membrance localized protein. Over-expression of ZmABCB15 enhanced the resistance by repressing the RBSDV replication ratio. ZmABCB15 might participate in the RBSDV resistance by affecting the homeostasis of active and inactive auxins in RBSDV infected seedlings. CONCLUSIONS: Polar auxin transport might participate in the RBSDV resistance by affecting the distribution of endogenous auxin among tissues. Our data showed the involvement of polar auxin transport in RBSDV resistance and provided novel mechanism underlying the auxin-mediated disease control technology.

Identification of genomic insertion and flanking sequences of the transgenic drought-tolerant maize line "SbSNAC1-382" using the single-molecule real-time (SMRT) sequencing method.

Safety assessment of genetically modified (GM) crops is crucial at the product-development phase before GM crops are placed on the market. Determining characteristics of sequences flanking exogenous insertion sequences is essential for the safety assessment and marketing of transgenic crops. In this study, we used genome walking and whole-genome sequencing (WGS) to identify the flanking sequence characteristics of the SbSNAC1 transgenic drought-tolerant maize line "SbSNAC1-382", but both of the two methods failed. Then, we constructed a genomic fosmid library of the transgenic maize line, which contained 4.18×105 clones with an average insertion fragment of 35 kb, covering 5.85 times the maize genome. Subsequently, three positive clones were screened by pairs of specific primers, and one of the three positive clones was sequenced by using single-molecule real-time (SMRT) sequencing technology. More than 1.95 Gb sequence data (~105× coverage) for the sequenced clone were generated. The junction reads mapped to the boundaries of T-DNA, and the flanking sequences in the transgenic line were identified by comparing all sequencing reads with the maize reference genome and the sequence of the transgenic vector. Furthermore, the putative insertion loci and flanking sequences were confirmed by PCR amplification and Sanger sequencing. The results indicated that two copies of the exogenous T-DNA fragments were inserted at the same genomic site, and the exogenous T-DNA fragments were integrated at the position of Chromosome 5 from 177155650 to 177155696 in the transgenic line 382. In this study, we demonstrated the successful application of the SMRT technology for the characterization of genomic insertion and flanking sequences.