Mapping quantitative trait loci for yield-related traits and predicting candidate genes for grain weight in maize

Abstract

Quantitative trait loci (QTLs) mapped in different genetic populations are of great significance for marker-assisted breeding. In this study, an F2:3 population were developed from the crossing of two maize inbred lines SG-5 and SG-7 and applied to QTL mapping for seven yield-related traits. The seven traits included 100-kernel weight, ear length, ear diameter, cob diameter, kernel row number, ear weight, and grain weight per plant. Based on an ultra-high density linkage map, a total of thirty-three QTLs were detected for the seven studied traits with composite interval mapping (CIM) method, and fifty-four QTLs were indentified with genome-wide composite interval mapping (GCIM) methods. For these QTLs, Fourteen were both detected by CIM and GCIM methods. Besides, eight of the thirty QTLs detected by CIM were identical to those previously mapped using a F2 population (generating from the same cross as the mapping population in this study), and fifteen were identical to the reported QTLs in other recent studies. For the fifty-four QTLs detected by GCIM, five of them were consistent with the QTLs mapped in the F2 population of SG-5 × SG-7, and twenty one had been reported in other recent studies. The stable QTLs associated with grain weight were located on maize chromosomes 2, 5, 7, and 9. In addition, differentially expressed genes (DEGs) between SG-5 and SG-7 were obtained from the transcriptomic profiling of grain at different developmental stages and overlaid onto the stable QTLs intervals to predict candidate genes for grain weight in maize. In the physical intervals of confirmed QTLs qKW-7, qEW-9, qEW-10, qGWP-6, qGWP-8, qGWP-10, qGWP-11 and qGWP-12, there were 213 DEGs in total. Finally, eight genes were predicted as candidate genes for grain size/weight. In summary, the stable QTLs would be reliable and the candidate genes predicted would be benefit for maker assisted breeding or cloning.

Identification of Gene Associated with Sweetness in Corn (Zea mays L.) by Genome-Wide Association Study (GWAS) and Development of a Functional SNP Marker for Predicting Sweet Corn

“…Molecular markers are used for the characterization of germplasms, identification and mapping of genes and QTLs for various agriculturally important traits in maize [ 31 , 32 , 33 , 34 , 35 , 36 ]. A previous study identified four simple sequence repeat (SSR) markers linked to the sh2 gene via bulk-segregant analysis (BSA) in three mapping populations [ 37 ].…”

QTL Analysis and Fine Mapping of a Major QTL Conferring Kernel Size in Maize (Zea mays)

“…The threshold of corrected P -value 0.005 and log 2 (Fold change) of 1 (absolute value) were considered as significantly differential expression. More information about the methods for reference genome index construction, paired-end clean reads alignment and count, FPKM calculation and DEGs analysis referred to our previous study ( Zhao and Su, 2019 ).…”

Genetic Architecture of Grain Yield-Related Traits in Sorghum and Maize

“…To date, over 168 primarily mapped QTLs associated with grain size have been reported in sorghum. Among them, 155 QTLs located on ten chromosomes have been mapped for thousand grain weight (TGW) in various independent studies published between 1995 and 2021 [ 13 , 34 , 43 , 45 , 46 , 47 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 ] ( Figure 1 a and Table S1 ). Few QTLs related to grain size (21 QTLs for grain length, 23 QTLs for grain width, and 26 QTLs for grain number per panicle) have been identified.…”