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Abstract The rich diversity of angiosperms, both the planet's dominant flora and the cornerstone of agriculture, is integrally intertwined with a distinctive evolutionary history. Here, we explore the interplay between angiosperm genome organization and botanical diversity, empowered by genomic approaches ranging from genetic linkage mapping to analysis of gene regulation. Commonality in the genetic hardware of plants has enabled robust comparative genomics that has provided a broad picture of angiosperm evolution and implicated both general processes and specific elements in contributing to botanical diversity. We argue that the hardware of plant genomes—both in content and in dynamics—has been shaped by selection for rather substantial differences in gene regulation between plants and animals such as maize and human, organisms of comparable genome size and gene number. Their distinctive genome content and dynamics may reflect in part the indeterminate development of plants that puts strikingly different demands on gene regulation than in animals. Repeated polyploidization of plant genomes and multiplication of individual genes together with extensive rearrangement and differential retention provide rich raw material for selection of morphological and/or physiological variations conferring fitness in specific niches, whether natural or artificial. These findings exemplify the burgeoning information available to employ in increasing knowledge of plant biology and in modifying selected plants to better meet human needs. 

Abstract Yield improvement in cotton could be accelerated through selection for functional yield drivers such as interception of cumulative photosynthetically active radiation (∑IPAR), radiation use efficiency (RUE), and harvest index (HI). However, information on the extent to which these traits vary in cotton in the southeastern United States is limited. It was hypothesized that functional yield drivers would vary significantly within a diverse cotton collection. This study was conducted in Tifton and Athens, GA, and included a total of 4 site‐years. Lint yield, total biomass production, ∑IPAR, RUE, and HI were all affected by genotype. Biomass was more strongly correlated with RUE than ∑IPAR. Even among the highest yielding genotypes, values for functional yield drivers (biomass and harvest index) differed significantly, indicating that high yields could be achieved by differentially manipulating these underlying traits. However, when considered for all genotypes, only HI exhibited a significant positive correlation with yield. Boll production and intra‐boll yield components were also affected by genotype. When considered across upland genotypes, lint per boll, lint per seed, and lint percent were strongly associated with HI and lint yield, whereas boll mass and seed number per boll were not. We conclude that the genotypes evaluated in the current study achieve high lint production per boll and lint yields by manipulating different yield drivers. However, lint yield was primarily maximized through an increase in HI due to increases in boll production and within‐boll distribution of biomass to fiber, not due to increases in total biomass production or boll size.