Among the 45 diploid species (2n = 2×=26) and 7 tetraploid species (2n = 4×=52) of cotton, Gossypium hirsutum (upland cotton) is the most widely cultivated worldwide [1]. Upland cotton is the most important source of natural fiber for the textile industry and accounts for 95% of the world’s cotton production [2, 3]. Besides, several by-products of cotton, such as fuzz fiber, cottonseed oil, and protein, are beneficial to human health, can serve as feed, and have important uses in several industries [4–6]. China is the largest cotton producer (22–25%) and consumer (more than 7.5 million tons annually) in the world (http://www.fao.org/faostat/). Traditionally, achieving high yields in cotton production has been labor-intensive, especially in China, with increased mechanization being offered as one of the solutions for increasing cotton yield. Improving fiber quality and early maturity based on the existing high-yield varieties has become an important breeding goal, aiming to meet the requirements for high-quality textiles and mechanization. In practice, there is a complex antagonistic effect among high yield, super quality fiber, and early maturity, and how to coordinate the relationships among these three traits is thus an issue of paramount importance in current cotton breeding and production programs [7–10].
Most yield-, fiber quality- and early maturity-related traits are regulated by minor-effect genes and have complex correlations [7–21]. For yield traits, a significant positive correlation was found between boll weight (BW) and seed index (SI), a significant negative correlation was found between SI and lint percentage (LP), and a variable correlation was identified between BW and LP [7, 22]. Regarding fiber quality traits, a significant positive correlation was detected between fiber length (FL) and fiber strength (FS), while micronaire (MC) was found to be significantly negatively correlated with FL and FS [7, 23, 24]. Significant positive correlations were found among early maturity traits, such as plant height (PH), node of the first fruiting branch (NFFB), height of NFFB (HNFFB), flowering timing (FT), flowering-to-boll opening period (FBP), and whole growth period (WGP) [25–27]. For yield and fiber quality traits, significant positive correlations were found between SI and FL and between BW and MC, while significant negative correlations were found between LP and FS and between LP and FL [7, 28]. For these three traits, the earlier maturity is achieved, the lower the yield and the poorer the fiber quality [8]. Traditional breeding methods have been inefficient at simultaneously accomplishing high yield, super fiber quality, and early maturity.
To date, many QTL relating to yield [29–31], fiber quality [23, 32–34], and maturity [25, 26, 35] have been mapped. Studies simultaneously focusing on yield and fiber quality revealed the existence of negative genetic correlations between these two traits [7, 36]. Zhang et al. identified six important QTL clusters containing both yield- and fiber quality-related QTL, and these exhibited opposing additive-effect directions [7]. For example, qClu-chr13-2 was associated with increased fiber quality but lower yield. Relatively few studies have concomitantly investigated cotton yield, fiber quality, and maturity [8, 37]. Eleven chromosomal segments were found to concurrently harbor QTL for yield, fiber quality, and early maturity; however, only three of these segments contained QTL with the same additive-effect direction, while the QTL in the other 8 segments showed opposite additive-effect directions [8]. Thus, more work is needed to reveal the molecular mechanisms underlying these traits and leverage them to break the unfavorable linkage between high yield, super fiber quality, and early maturity.
Many candidate genes have been identified through QTL mapping and map-based cloning. For example, GbCML7 was suggested to regulate boll number (BN) in some backgrounds [38], TIP41L [39] and GhDA1-1A [40] were speculated to be the putative candidate genes responsible for both cotton seed size and boll weight, while Gh_D01G0162, Gh_D07G0465 [41], and GB_A07G1034 [42] were identified as candidate LP-determining genes. For fiber quality, Ghir_A10G022020 was proposed to act as a negative regulator of FL by interacting with NF-YA [43], whereas GB_D11G3437, GB_D11G3460, and GB_D11G3471 were found to be associated with FS [42]. For early maturity, GhAP1-D3 was reported to positively regulate flowering time and early maturity without affecting yield and fiber quality [44]. However, the current pool of genes known to be involved in the development of these traits in cotton cannot meet the needs of molecular design breeding.
In this study, to unearth additional information regarding the genetic relationships among high yield, super fiber quality, and early maturity, a total of 16 traits were investigated in four consecutive generations, and these traits were used for QTL mapping to identify outstanding QTL and regions with overlapping QTL based on a high-density genetic map [29]. Candidate genes for these traits in the outstanding QTL and QTL overlapping regions were analyzed using published RNA-seq data. Additionally, the expression patterns of the identified candidate genes were analyzed by qRT-PCR.