QTL Mapping Based on Different Genetic Systems for Essential Amino Acid Contents in Cottonseeds in Different Environments

et al. (2013) QTL Mapping Based on Different Genetic Systems for Essential Amino Acid Contents in Cottonseeds in Different Environments. PLoS ONE 8(3): e57531. doi:10.1371/journal.pone.0057531 QTL Mapping Based on Different Genetic Systems for Essential Amino Acid Contents in Cottonseeds in Different Environments Haiying Liu. 0 Alfred Quampah. 0 Jinhong Chen 0 Jinrong Li 0 Zhuangrong Huang 0 Qiuling He 0 Shuijin Zhu 0 Chunhai Shi 0 Tianzhen Zhang, Nanjing Agricultural University, China 0 Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University , Hangzhou , People's Republic of China Cottonseeds are rich in various essential amino acids. However, the inheritance of them at molecular level are still not defined across various genetic systems. In the present study, using a newly developed mapping model that can analyze the embryo and maternal main effects as well as QTL 6 environment interaction effects on quantitative quality trait loci (QTLs) in cottonseeds, a study on QTL located in the tetraploid embryo and tetraploid maternal plant genomes for essential amino acid contents in cottonseeds under different environments was carried out, using the immortal F2 (IF2) populations from a set of 188 recombinant inbred lines derived from an intraspecific hybrid cross of two upland cotton germplasms HS46 and MARKCBUCAG8US-1-88 as experimental materials. The results showed a total of 35 QTLs associated with these quality traits in cottonseeds. Nineteen QTLs were subsequently mapped on chromosome 5, 6 and 8 in sub-A genome and chromosome 15, 18, 22 and 23 in sub-D genome. Eighteen QTLs were also found having QTL 6 environment (QE) interaction effects. The genetic main effects from QTLs located on chromosomes in the embryo and maternal plant genomes and their QE effects in different environments were all important for these essential amino acids in cottonseeds. The results suggested that the influence of environmental factors on the expression of some QTLs located in different genetic systems should be considered when improving for these amino acids. This study can serve as the foundation for the improvement of these essential amino acids in cottonseeds. - Funding: The project is support by the National Basic Research Program (973 program. No: 2010CB126006) and the National High Technology Research and Development Program of China (2011AA10A102). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. . These authors contributed equally to this work. Cotton (Gossypium hirsutum L) is a leading fiber crop in the world producing annually both natural fiber and cottonseeds in large quantities. OBrien et al. (2005) [1] reported that 1.65 kg of cottonseeds could be gained for every 1 kg of lint yielded. Cottonseed kernel is the most nutritious part possessing high oil (28.2444.05%) and protein (27.8345.6%) contents [2]. To date, cottonseed oil has been principally used for human consumption, while its protein part for animal feed production. Literature reports the availability of seventeen different kinds of amino acids including essential amino acids like isoleucine, leucine, threonine, methionine, phenylalanine, and lysine in cottonseeds [3,4]. With the growing world population, the potential for its use as an important source of food is fairly high. For this reason, the improvement on cottonseed quality traits including its amino acid content by genetic breeding is becoming the need of hour. Currently, most of the studies on cottonseeds have been focused on oil and gossypol contents [5], [6] with less emphasis on amino acids. Cherry et al. [7] observed that total amino acid content was mainly controlled by the genotype. Ji et al. [8] analyzed the genetic effects on amino acid content in the seeds of upland cotton and suggested that most amino acid compositions were mainly affected by the dominance effect. Song and Zhang [9] identified QTL for seven amino acids using molecular marker technique, which was carried out only on one genetic system, i.e. embryo genome. Though cottonseed is a new generation and different from its maternal plant, it still depends on assimilates from the maternal plant during seed development. This suggests that the genetic mechanism of cottonseed quality traits could be directly or indirectly affected by the genetic behavior of maternal plant. That is why the genetic research on cottonseeds is very difficult. Researchers have also reported that cottonseed quality traits are simultaneously controlled by the genetic main effects from different genetic systems including tetraploid embryo and tetraploid maternal plant nuclear genes, as well as their genotype 6 environment (GE) interaction effects [10]. These reports also suggest that genetic effects related to amino acid content in cottonseeds could be further analyzed based on different genetic systems at the molecular level. Similar studies have been successfully conducted on rice [11], [12]. The analysis of seed quality traits based on the two genetic systems can help further reveal the genetic basis of amino acid content in cottonseeds and serve as the foundation for its quality improvement as a food or feed product. Amino acids are principally divided into two groups, essential and non-essential. Essential amino acids play a crucial role in the metabolic processes which make the body grow normally but cannot be synthesized in the human body and must be obtained from the foods been eaten [13]. In the present study, investigations to identify QTLs governing essential amino acids except for tryptophan in cottonseeds were conducted using the newly developed QTL mapping method that could analyze embryo and maternal main effects and their QE effects on quantitative traits of seeds in dicotyledonous crops. Seeds of immortal F2 populations used in this experiment were obtained from random crosses among a set of 188 RILs. This RIL population which has been successfully used in various genetic studies on cotton [1418] was derived from a hybrid of HS46 and MARKCBUCAG8US-188. In this study, the genetic effects including the embryo additive main effect (ae), embryo dominance main effect (de), maternal additive main effect (am) and their environmental interactions were analyzed. This work was aimed at revealing in depth the genetic mechanisms of QTLs for essential amino acids, which provide the foundation for the improvement of these essential amino acids in cottonseeds. Phenotypic performance of essential amino acids in cottonseeds Phenotypic values for essential amino acid contents of the two parents, HS46 and MARKCBUCAG8US-1-88, and the IF2 population in 2009 and 2010 are summarized on Table 1. Significant differences between HS46 and MARKCBUCAG8US1-88 were detected for these traits in two years. The contents of seven essentia (...truncated)