Abstract
We describe a comprehensive quantitative trait locus (QTL) analysis for 24 main agronomic traits of cabbage. Field experiments were performed using a 196-line double haploid population in three seasons in 2011 and 2012 to evaluate important agronomic traits related to plant type, leaf, and head traits. In total, 144 QTLs with LOD threshold >3.0 were detected for the 24 agronomic traits: 25 for four plant-type-related traits, 64 for 10 leaf-related traits, and 55 for 10 head-related traits; each QTL explained 6.0–55.7% of phenotype variation. Of the QTLs, 95 had contribution rates higher than 10%, and 51 could be detected in more than one season. Major QTLs included Ph 3.1 (max R2 = 55.7, max LOD = 28.2) for plant height, Ll 3.2 (max R2 = 31.7, max LOD = 13.95) for leaf length, and Htd 3.2 (max R2 = 28.5, max LOD = 9.49) for head transverse diameter; these could all be detected in more than one season. Twelve QTL clusters were detected on eight chromosomes, and the most significant four included Indel481–scaffold18376 (3.20 Mb), with five QTLs for five traits; Indel64–scaffold35418 (2.22 Mb), six QTLs for six traits; scaffold39782–Indel84 (1.78 Mb), 11 QTLs for 11 traits; and Indel353–Indel245 (9.89 Mb), seven QTLs for six traits. Besides, most traits clustered within the same region were significantly correlated with each other. The candidate genes at these regions were also discussed. Robust QTLs and their clusters obtained in this study should prove useful for marker-assisted selection (MAS) in cabbage breeding and in furthering our understanding of the genetic control of these traits.
Highlights
Selection based on breeding objects is a key step in the crop breeding process
We evaluated 24 main agronomic traits in three seasons based on a 196-line double haploid (DH) population, and for the first time in heading cabbage, mapped significant regions of quantitative trait locus (QTL) clusters associated with these traits and analyzed the candidate genes
Some trait values for the DH population showed inter-parent variations or were similar to one parental line, while others exhibited bi-directional transgressive variations, suggesting alleles with additive effects or complementation effect for these traits were distributed among the parents
Summary
Selection based on breeding objects is a key step in the crop breeding process. Traditional selection mostly relies on the phenotype, i.e., the field performance of agronomic traits; this is time-consuming and costly, cannot differentiate between heterozygous and homozygous plants, and can be affected by the environment. Before the reference genome sequence of B. oleracea was made public in 2014 (Liu et al, 2014), QTLs were mapped to linkage groups rather than to chromosomes, using amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism (RFLP), and random-amplified polymorphic DNA (RAPD) markers, etc These aforementioned methods have been used for identification of QTLs associated with clubroot resistance (Landry, 1992; Voorrips et al, 1997; Nagaoka et al, 2010), black rot disease resistance (Camargo and Champagne, 1995), stem-related traits (Kennard et al, 1994), flowering time (Bohuon et al, 1998; Okazaki et al, 2007; Uptmoor et al, 2008), fertility (Wang et al, 2000), plant size (Lan and Paterson, 2001), regeneration capability of tissue culture in Agrobacterium-mediated transformation (Sparrow et al, 2004; Oldacres et al, 2005), water absorption and photosynthetic utilization efficiency (Hall et al, 2005), regeneration capability of protoplast (Holme et al, 2004), and seed germination rate under a 5% oxygen supply (Finch-Savage et al, 2005). Numerous agronomic traits important for cabbage breeders, such as plant-type and leaf-related traits, have seldom been investigated
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