Research Article: Genome-wide haplotype-based association analysis of key traits of plant lodging and architecture of maize identifies major determinants for leaf angle: hapLA4

Date Published: March 6, 2019

Publisher: Public Library of Science

Author(s): Carlos Maldonado, Freddy Mora, Carlos A. Scapim, Marlon Coan, Maoteng Li.

http://doi.org/10.1371/journal.pone.0212925

Abstract

Traits related to plant lodging and architecture are important determinants of plant productivity in intensive maize cultivation systems. Motivated by the identification of genomic associations with the leaf angle, plant height (PH), ear height (EH) and the EH/PH ratio, we characterized approximately 7,800 haplotypes from a set of high-quality single nucleotide polymorphisms (SNPs), in an association panel consisting of tropical maize inbred lines. The proportion of the phenotypic variations explained by the individual SNPs varied between 7%, for the SNP S1_285330124 (located on chromosome 9 and associated with the EH/PH ratio), and 22%, for the SNP S1_317085830 (located on chromosome 6 and associated with the leaf angle). A total of 40 haplotype blocks were significantly associated with the traits of interest, explaining up to 29% of the phenotypic variation for the leaf angle, corresponding to the haplotype hapLA4.04, which was stable over two growing seasons. Overall, the associations for PH, EH and the EH/PH ratio were environment-specific, which was confirmed by performing a model comparison analysis using the information criteria of Akaike and Schwarz. In addition, five stable haplotypes (83%) and 15 SNPs (75%) were identified for the leaf angle. Finally, approximately 62% of the associated haplotypes (25/40) did not contain SNPs detected in the association study using individual SNP markers. This result confirms the advantage of haplotype-based genome-wide association studies for examining genomic regions that control the determining traits for architecture and lodging in maize plants.

Partial Text

Maize (Zea mays L.), along with rice and wheat, is one of the most important agricultural crops worldwide [1] and has been used as a food source [2] and as a raw material for pharmaceutical and agroindustrial products [1, 3], because of its nutritional composition (72% starch, 10% protein and 4% fat), versatility and broad adaptability. Usually, maize breeding programs have focused on obtaining gains in grain yield [4, 5]. However, the selection of cultivars based on traits related to lodging and the architecture of the plants has allowed important genetic advances in various breeding programs [1, 6, 7, 8, 9, 10, 11, 12, 13]. In fact, traits such as plant height (PH), ear height (EH) and the EH/PH ratio (or PH/EH) have important effects on plant lodging in intensive maize cultivation systems [12]. In addition, leaf angle (LA), an important determinant for the plant architecture, has been significantly improved over recent decades to adapt to the current planting density requirements, which has increased maize production [9]. Therefore, a better understanding of the genetic architecture of these traits would help during the processes of selecting and/or developing highly productive cultivars (or lines or hybrids).

According to the information criteria, the model that best fits the PH, EH and EH/PH data was the complete model (M3), which includes the effect of line-season (LxS) interaction (Table 1), while for LA, the model without LxS interaction (M2) was the best fit model. Moreover, based on the results of AIC, it was determined that there were no differences between the M2 and M3 models (Δi<2) [55] for LA. The moderate coefficients of variation (CV) found in the four traits (19% in LA, 10% in PH, 16% in EH and 11% in the EH/PH ratio) indicate an adequate level of experimental precision. The average values for PH (1.52 and 1.27, respectively) and EH (0.81 and 0.58, respectively) differed between growing seasons, with higher values observed during 2014–2015, indicating that the environment had an impact on variation for these traits. On the other hand, the LA trait did not show significant changes between seasons (1.287 and 1.291, for 2014–2015 and 2015–2016, respectively). The high values of heritability (H2 = 0.95, 0.74, 0.94 and 0.83, for PH, LA, EH and the EH/PH ratio, respectively) were similar to those reported in previous studies [1, 7, 15, 56]. The strong genetic control observed in this maize panel increases the detection power of genetic regions associated with the traits [57].   Source: http://doi.org/10.1371/journal.pone.0212925

 

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