Lignocellulosic biomass from fast-growing plantation trees is composed of carbohydrate-rich materials deposited into plant cell walls in a coordinated manner during wood formation. The diversity and evolution of the transcriptional networks regulating this process have not been studied extensively. We investigated patterns of species-level nucleotide diversity in the -2 -promoters of cellulose synthase (CesA) genes from different Eucalyptus tree species and assessed the possible roles of DNA sequence polymorphism in the gain or loss of ciselements harboured within the promoters. Promoter regions of three primary and three secondary cell wall-associated CesA genes were isolated from 13 Eucalyptus species and were analysed for nucleotide and cis-element diversity. Species-level nucleotide diversity (π) ranged from 0.014 to 0.068 and different CesA promoters exhibited distinct patterns of sequence conservation. A set of 22 putative cis-elements were mapped to the CesA promoters using in silico methods. Forty two percent of the mapped cis-element occurrences contained singleton polymorphisms which resulted in either the gain or loss of a cis-element in a particular Eucalyptus species. The promoters of Eucalyptus CesA genes contained regions that are highly conserved at the species (Eucalyptus) and genus (with Arabidopsis and Populus) level, suggesting the presence of regulatory modules imposing functional constraint on such regions. Nucleotide polymorphisms in the CesA promoters more frequently created new cis-element occurrences than disrupted existing cis-element occurrences, a process which may be important for the maintenance and evolution of cellulose gene regulation in plants.
Opuntia ficus-indica (L.) Mill. is one of the most recognisable agricultural crops that can withstand harsh environmental conditions. South Africa is one of the few countries that hosts a large germplasm of Opuntia cultivars that represent an ex-situ conservation population. However, little is known about the genetic diversity in this population. Additionally, some genotypes are morphologically indistinct, and therefore, making it a challenge for novice farmers and researchers to recognise specimens in the germplasm. The current study aimed to differentiate and measure the genetic diversity in 44 cultivars that represent the South African Opuntia germplasm using eight SSR markers. Evidently, the cultivars comprised moderate levels of diversity (average polymorphic information content, PIC = 0.37, Nei’s unbiased gene diversity = 0.42) that discriminated 90% of the cultivars. Analysis of the cultivars with the unweighted pair-group method using arithmetic averages (UPGMA) method revealed three main clusters, whereas principal coordinate analysis (PCoA) showed indistinct clustering of cultivars based on their usage in the agricultural market. Overall, the used SSR markers were able to distinguish most cultivars in the South African Opuntia germplasm – a genetic resource that appears to hold sufficient genetic diversity to aid the conservation and breeding of novel cultivars for the agriculture market.
Opuntia ficus-indica (L.) Mill. is one of the most recognisable agricultural crops that can withstand harsh environmental conditions. South Africa is one of the few countries that hosts a large germplasm of Opuntia cultivars, which represent an ex-situ conservation population. However, little is known about the genetic diversity in this population. Additionally, some genotypes are morphologically indistinct, and therefore, making it a challenge for novice farmers and researchers to recognise specimens in the germplasm. The current study aimed to differentiate and measure the genetic diversity in 44 cultivars that represent the South African Opuntia germplasm using eight simple sequence repeat (SSR) markers. Evidently, the cultivars comprised moderate levels of diversity (average polymorphic information content, PIC = 0.37, Nei’s unbiased gene diversity = 0.42) that discriminated 90% of the cultivars. Analysis of the cultivars with the unweighted pair-group method using arithmetic averages (UPGMA) method revealed three main clusters, whereas principal coordinate analysis (PCoA) showed indistinct clustering of cultivars based on their usage in the agricultural market. Overall, the used SSR markers were able to distinguish most cultivars in the South African Opuntia germplasm—a genetic resource that appears to hold sufficient genetic diversity to aid the conservation and breeding of novel cultivars for the agriculture market.
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