Association mapping of seed oil and protein contents in upland cottonby Guizhen Liu, Hongxian Mei, Sen Wang, Xinghe Li, Xiefei Zhu, Tianzhen Zhang



Agronomy and Crop Science / Horticulture / Plant Science / Genetics


Association mapping of seed oil and protein contents in upland cotton

Guizhen Liu . Hongxian Mei .

Sen Wang . Xinghe Li . Xiefei Zhu .

Tianzhen Zhang

Received: 26 November 2014 / Accepted: 15 April 2015  Springer Science+Business Media Dordrecht 2015

Abstract Linkage disequilibrium-based association mapping is a powerful tool for dissecting the genetic basis underlying complex traits. In this study, an association mapping panel consisting of 180 elite

Upland cotton cultivars was constructed, evaluated in three locations across 2 years and genotyped using 228

SSRs to detect molecular markers associated with seed oil and protein contents. A total of 86 significant (a´ = 0.01) marker-trait associations were detected between 58 SSR markers and two seed quality traits in six environments. Fifteen SSR markers distributed on ten chromosomes (A3, A7, A9, A10, A12, A13, D2,

D5, D6 and D9) and 12 across 9 chromosomes (A3,

A7, A9, A10, A12, D2, D3, D5 and D9) associated with seed oil and protein contents, respectively, could be detected in more than one environment. Among the 18 SSR markers significantly associated with seed oil and/or protein contents, nine loci were associated with both seed traits simultaneously. The results of this study provide useful information for further understanding the genetic basis of cottonseed oil and protein traits, and they should facilitate future efforts to breed cotton containing seeds with high oil or high protein contents using MAS.

Keywords Upland cotton  Seed oil  Seed protein 

SSR  Association mapping


Gossypium hirsutum L., commonly referred to as

Upland cotton, is an essential cash crop worldwide, which accounts for 95 % of the world’s cotton production (Zhang et al. 2008). Commercial seed cotton is composed of approximately 40 % lint and 60 % seed, which provides the most important natural fiber for the textile industry as well as seed nutrition for both humans and livestock. The importance of fiber quality has long been recognized due to the changing requirements of spinning technology, and considerable efforts have been devoted to improving fiber quality traits (Chen et al. 2011; Ashokkumar et al. 2014). By contrast, cottonseed is still considered to be a by-product of lint, and little emphasis has been

Guizhen Liu and Hongxian Mei have contributed equally to this work.

Electronic supplementary material The online version of this article (doi:10.1007/s10681-015-1450-z) contains supplementary material, which is available to authorized users.

G. Liu  S. Wang  X. Li  X. Zhu  T. Zhang (&)

National Key Laboratory of Crop Genetics and

Germplasm Enhancement, MOE Hybrid Cotton R & D

Engineering Research Center, Nanjing Agricultural

University, Nanjing 210095, China e-mail:

H. Mei

Sesame Research Centre, Henan Academy of Agricultural

Sciences, Zhengzhou 450002, China 123


DOI 10.1007/s10681-015-1450-z placed on breeding for seed nutritional components (Wu et al. 2009). Cottonseed oil, which consists of approximately 70 % unsaturated and 30 % saturated fatty acids, can be refined to eliminate phenolic compounds, which can then directly be used for edible purposes (Lukonge et al. 2007), and it is also considered to be an important biofuel resource (Liu et al. 2009).

Cottonseed protein is widely used to feed sheep, cattle and other ruminant livestock (Kohel et al. 1985;

Coppock et al. 1987). If gossypol were eliminated from cottonseed protein, it would be fully edible, thereby providing a new, important source of nutrition, which would increase food security worldwide.

Cottonseed oil and protein contents are quantitative traits that are simultaneously affected by genetic and environmental factors during seed development; these traits often vary among different growing seasons, locations and years (Dani and Kohel 1989; Wu et al. 2010). Large-scale, repeated chemical testing during breeding is labor-intensive, costly and time-consuming, and it has proven to be unfeasible for effectively improving these two traits based simply on phenotypic selection (Wu et al. 2010; Ashokkumar and Ravikesavan 2011). Molecular markers tightly linked to target genes and/or QTLs can be used for markerassisted selection (MAS), which markedly improves breeding efficiency (Xu and Crouch 2008; Ashokkumar and Ravikesavan 2011). In the past two decades, the availability of abundant molecular markers has made tagging QTLs harboring functional genes through family-based linkage mapping a routine process, and a large number of QTLs for agronomically important traits have been identified in cotton (Zhang et al. 2008; Said et al. 2013), including QTLs for cottonseed oil and protein (Song and Zhang 2007;

An et al. 2010; Liu et al. 2012; Alfred et al. 2012; Yu et al. 2012; Liu et al. 2013). However, approximately 80 % of the QTLs identified by linkage mapping could not be confirmed in subsequent studies, and few have actually been applied in breeding programs (Lacape et al. 2010; Said et al. 2013). This may be due to the fact that most of the QTLs were population-specific, and the limited amount of recombination present in most populations used for linkage mapping makes it difficult to map QTLs at a high resolution, which has severely limited their application in breeding programs. Linkage disequilibrium (LD)-based association mapping (AM), which has the potential to exploit most recombination events that have occurred during the plant’s evolutionary history and to simultaneously evaluate the effects of many alleles of target loci, has become a powerful approach to dissecting complex traits in many crops (Zhu et al. 2008; Mackay et al. 2009). In cotton, AM had been used for QTL detection for fiber quality traits (Kantartzi and Stewart 2008; Abdurakhmonov et al. 2008, 2009; Zeng et al. 2009; Zhang et al. 2013; Cai et al. 2014), yield and its components (Zhang et al. 2013; Mei et al. 2013), disease resistance (Mei et al. 2014; Zhao et al. 2014) and salinity tolerance (Saeed et al. 2014). However, to date, to the best of our knowledge, no associationmapping study of seed oil and protein traits has been reported in cotton. In the present study, 180 elite