A comprehensive meta-analysis of plant morphology, yield, stay-green, and virus disease resistance QTL in maize (Zea mays L.)

Abstract

The meta-QTL and candidate genes will facilitate the elucidation of molecular bases underlying agriculturally important traits and open new avenues for functional markers development and elite alleles introgression in maize breeding program. A large number of QTLs attributed to grain productivity and other agriculturally important traits have been identified and deposited in public repositories. The integration of fruitful QTL becomes a major issue in current plant genomics. To this end, we first collected QTL for six agriculturally important traits in maize, including yield, plant height, ear height, leaf angle, stay-green, and maize rough dwarf disease resistance. The meta-analysis method was then employed to retrieve 113 meta-QTL. Additionally, we also isolated candidate genes for target traits by the bioinformatic technique. Several candidates, including some well-characterized genes, GA3ox2 for plant height, lg1 and lg4 for leaf angle, zfl1 and zfl2 for flowering time, were co-localized with established meta-QTL intervals. Intriguingly, in a relatively narrow meta-QTL region, the maize ortholog of rice yield-related gene GW8/OsSPL16 was believed to be a candidate for yield. Leveraging results presented in this study will provide further insights into the genetic architecture of maize agronomic traits. Moreover, the meta-QTL and candidate genes reported here could be harnessed for the enhancement of stress tolerance and yield performance in maize and translation to other crops.

Quantitative trait locus analysis of heterosis for plant height and ear height in an elite maize hybrid zhengdan 958 by design III

“…f Heterosis-associated QTLs reported in previous studies: 1 Ku et al [43]; 2 Wen et al [48]; 3 Yang et al [45]; 4 Wang et al [18]; 5 Frascaroli et al [46]; 6 Song et al [22]; 7 Frascaroli et al [23]; 8 Li et al [16]…”

“…Red shadows on the physical map indicate the corresponding positions of each QTL. The verticals in different colors alongside the physical map indicate known heterotic-related QTLs from different studies (1 Ku et al [43]; 2 Wen et al [48]; 3 Yang et al [45]; 4 Wang et al [18]; 5 Frascaroli et al [46]; 6 Song et al [22]; 7 Frascaroli et al [23]; 8 Li et al [16]). The known positions of br2 , an1 , brd1 , d8 , d9 , td1 , clt1 and d3 are presented in blue arrows …”

“…The plus (“+”) signs within the brackets indicate Chang 7–2 contributed increasing alleles c QTL information for the combined analysis d Degree of dominance: A, additive (| d i * / a i * | ≤ 0.20); PD, partial dominance (0.20 < | d i * / a i * | < 0.80); D, dominance (0.80 ≤ | d i * / a i * | < 1.20); and OD, overdominance (| d i * / a i * | ≥ 1.20) e C Indicates the combined QTL analysis based on the BLUP values across five environments f Heterosis-associated QTLs reported in previous studies: 1 Ku et al [43]; 2 Wen et al [48]; 3 Yang et al [45]; 4 Wang et al [18]; 5 Frascaroli et al [46]; 6 Song et al [22]; 7 Frascaroli et al [23]; 8 Li et al [16]…”

“…Wang et al integrated QTLs for plant height and ear height based on the target map IBM2 2008 Neighbors. They found several GA pathway genes were located in the meta-QTL region [18]. Xing et al cloned a major plant height QTL- qph1 , which contains a naturally occurring rare SNP in br2.…”

Unraveling the molecules hidden in the gray shadows of quantitative disease resistance to pathogens

“…This is the challenge of statistical QTL meta-analyses. The detection of common QTLs and the identification of co-locating resistance candidate genes from different experiments and populations have been recently achieved using QTL metaanalyses in maize to find resistance genes for virus diseases (Wang et al, 2016), leaf rust in wheat (Soriano and Royo, 2015) and verticillium wilt in cotton .…”