The integrity of the seed coat is an important attribute to maintain seed quality until it is time to plant. However, certain anatomical structure conditions may interfere with the physiological activities necessary for germination. A coat that is too hard with a lignified chalazal cap, also called “hard-seed”, could constrain the embryo and reduce water absorption, preventing germination ^{[12][21][22][23]}[21,30,31,32]. This trait is uncommon in modern cotton varieties due to selections and breeding but is often seen in wild-type species. Seed coat water impermeability is often classified as physical dormancy, and it is caused by impermeable layers of palisade cells ^[24][25][26][8,33,34]. Christiansen and Moore ^[21][30] conducted microscopic studies to compare the structure of the cotton seed coats of hard seeds versus non-hard seeds. They found that in hard seeds, the structures near the chalazal area are highly compacted in comparison to the other seeds. There are some studies on different techniques to increase seed coat permeability and water absorption to boost cotton seed germination in a research environment. For example, soaking cotton seeds in hot water (80 °C to 85 °C) for at least one minute was found to improve the germination of dormant hard seeds ^[21][27][30,35]. Scarification of the seed coat is another approach common in many species that have water impermeable seeds ^[22][28][31,36]. Mechanical scarification, an abrasion method that removes part of the seed coat, is often used in legume crops ^[28][36]. The intensity of scarification can be regulated in commercial scarifiers to avoid more than necessary damage to the seed, and consequent injuries to the embryo. A study of different mechanical scarification treatments in cicer milkvetch (Astralagus cicer) reported greater germination in scarified seeds, although field stands were affected in treatments where seeds were “over-scarified” ^[29][37]. Mechanical scarification of cotton seed using a commercial seed scarifier has been attempted ^[18][27], but field emergence and establishment were affected. However, a small rupture on the cotton seed coat has been reported to aid in the germination of hard-seeded species by allowing the seed to absorb water efficiently ^[21][30][30,38]. Acid delinting is another known scarification method for expediting germination in several plant species, including cotton ^[31][39]. Marani and Amirav ^[32][40] reported improved and quicker germination of cotton at low temperatures after acid delinting. In more recent germination experiments, melatonin seed treatment has been reported to regulate the opening of stomata in the seed coat increasing germination rates in cotton seeds ^[33][41]. Studies on cold plasm treatment and its mechanisms that lead to a biological response in seeds showed an increase in seed water absorption, improved warm germination, and chilling tolerance in cotton ^[34][35][42,43].

Extreme water shortages can significantly constrain germination and seedling establishment of most field crops ^[36][44]. Although cotton is relatively tolerant to drought compared to other agricultural crops, marginal soil moisture can decrease germination rates. The process of imbibition that initiates germination is contingent on the water potential difference between the seed and the soil ^[37][45]. If water is scarce, internal seed moisture tension is weakened and water uptake may decrease. Moreover, hydration rates can be affected by other environmental conditions such as low temperatures, and those can vary among cotton species ^[8][17]. In one study, Gossypium hirsutum was found to have a lower hydration rate than Gossypium barbadense when seeds were subjected to various levels of chilling ^[38][46]. Drought-tolerant species and varieties, among other characteristics, may have developed mechanisms that facilitate seed water imbibition. These can include adaptations in the seed coat like increased water permeability, quick water intake, and different amounts of water requirements for germination. Stiles ^[39][47] reported seed adaptability in low water environments in drought-tolerant cotton and corn varieties. For those reasons, in greenhouse studies when different cotton species and seed sources are often used, it is important to consider that standardizing water treatments may result in variable seed germination responses.

Chilling temperatures can injure germinating cotton seeds, especially during the first stages of imbibition when seeds start soaking up water and are at their most sensitive phase ^[8][40][17,48]. Cold soil temperatures during this period can ultimately kill the embryo or cause long-term adverse consequences to the growing plant, like undeveloped tap root, delayed maturity, and ultimately lower yields ^[41][42][43][49,50,51]. Krzyzanowski and Delouche ^[44][52] used different lots of a commercial G. hirsutum cotton variety to report an optimal germination temperature of 28 °C to 30 °C, with significantly lower germination percentages when the temperature dropped below 20 °C. Ludwig ^[45][53] in 1932 indicated that upland cotton germination would be unlikely in temperatures lower than 11 °C.

Germination potential peak usually occurs shortly after harvest and decreases exponentially with long-term storage time. A decline in seed vigor and viability may be caused by a variety of biochemical processes in the seed that can be accelerated under inappropriate temperature and moisture conditions ^{[46][47][48][49][50][51]}[54,55,56,57,58,59]. Most seed species preserve their viability best when dried and stored in low moisture content. However, according to an early 1900s study, cotton seeds that are stored in extremely dry conditions and seed moisture content falls below 6%, have an increased chance of becoming hard-seeded and germination will be affected. According to the authors, an approximate 12% moisture content in the seed is necessary for vigorous germination ^[20][29]. Low-temperature cold storage (0–5 °C) is also desirable for the retention of seed quality ^[11][20]. Therefore, proper seed storage conditions are essential to maintain viable seed stock in a research program.

Dormancy can be caused by numerous factors and manifested in seasonal cycles according to environmental determinants; it is generally defined as the failure of a viable seed to germinate under favorable conditions ^[13][52][22,60]. There are two widely accepted distinctions in the dormancy cycle—primary dormancy and secondary dormancy. The prevention of germination in freshly harvested mature seeds caused by abscisic acid during seed development is denominated in primary dormancy ^[53][54][61,62]. This usually requires a combination of events to reinstate full metabolic activity, such as changes in temperature, moisture variation, or simply the passage of time ^[55][63]. Nevertheless, dispersed seeds could also enter a second state of dormancy when environmental factors are not as propitious to germination, also known as secondary dormancy ^[52][60]. According to Bewley and Black ^[11][20], mature seeds can enter a dormant state after imbibition and can survive fully imbibed for a long period of time. Taylor and Lankford ^[56][64] reported secondary dormancy in cotton under low temperature and high salinity stress in the 1970s.

In modern agricultural crops, due to primary dormancy, seeds are rarely planted immediately after harvest. Early studies in cotton described an increase in germination when cotton seeds were submitted to air-drying and short-term storage before planting in comparison to freshly harvested seeds. ^[57][65]. Although it may seem disadvantageous in agricultural crops, at a first glance, for fresh seeds to halt germination, this adaptive mechanism could prevent a circumstance called preharvest sprouting in which seeds prematurely germinate while still attached to the parental plant causing tremendous economic loss ^[13][22].