Sorghum bicolor, a photosynthetically efficient C4 grass, represents an important source of grain, forage, fermentable sugars, and cellulosic fibers that can be utilized in myriad applications ranging from bioenergy to bioindustrial feedstocks. Sorghum’s efficient fixation of carbon per unit time per unit area per unit input has led to its classification as a preferred biomass crop highlighted by its designation as an advanced biofuel by the U.S. Department of Energy. Due to its extensive genetic diversity and worldwide colonization, sorghum has considerable diversity for a range of phenotypes influencing productivity, composition, and sink/source dynamics. To dissect the genetic basis of these key traits, we present a sorghum carbon-partitioning nested association mapping population generated by crossing 11 diverse founder lines with Grassl as the single recurrent female. By exploiting existing variation among cellulosic, forage, sweet and grain sorghum carbon partitioning regimes, the sorghum carbon-partitioning nested association mapping population will allow the identification of important biomass-associated traits, elucidate the genetic architecture underlying carbon partitioning and improve our understanding of the genetic determinants affecting unique phenotypes within Poaceae. We contrast this nested association mapping population with an existing grain population generated using Tx430 as the recurrent female. Genotypic data are assessed for quality by examining variant density, nucleotide diversity, linkage decay, and is validated using pericarp and testa phenotypes to map known genes affecting these phenotypes. We release the 11-family nested association mapping population along with corresponding genomic data for use in genetic, genomic, and agronomic studies with a focus on carbon-partitioning regimes.
Simple sugars are the essential foundation to plant life, and thus, their production, utilization, and storage are highly regulated processes with many complex genetic controls. Despite their importance, many of the genetic and biochemical mechanisms remain unknown or uncharacterized. Sorghum, a highly productive, diverse C 4 grass important for both industrial and subsistence agricultural systems, has considerable phenotypic diversity in the accumulation of nonstructural sugars in the stem. We use this crop species to examine the genetic controls of high levels of sugar accumulation, identify genetic mechanisms for the accumulation of nonstructural sugars, and link carbon allocation with iron transport. We identify a species-specific tandem duplication event controlling sugar accumulation using genome-wide association analysis, characterize multiple allelic variants causing increased sugar content, and provide further evidence of a putative neofunctionalization event conferring adaptability in Sorghum bicolor. Comparative genomics indicate that this event is unique to sorghum which may further elucidate evolutionary mechanisms for adaptation and divergence within the Poaceae. Furthermore, the identification and characterization of this event was only possible with the continued advancement and improvement of the reference genome. The characterization of this region and the process in which it was discovered serve as a reminder that any reference genome is imperfect and is in need of continual improvement. 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 KEYWORDS Neofunctionalization; Duplication; Carbon partitioning;Poaceae; Adaptation The continued existence of biology on Earth is largely depen-1 dent on the creation of sugar generated through carbon fixation. 2 As one of the most fundamental sources of energy for life, under-3 standing the biological controls of the synthesis and regulation of 4 sugar flux in plants is critical for the continued improvement of 5 agricultural productivity regardless of system. Sugar is not only 6 used as a source of energy for plant cells, but it is also used as a sig-7 naling molecule for key developmental and physiological changes 8 spanning the life cycle of the plant. Sugar and its myriad biolog-9 ical regulators and sensors are linked to seed development and 10 growth, hormone signaling, carbon metabolism, stress response 11
Sorghum has been considered a recalcitrant plant in vitro and suffers from a lack of regeneration protocols that function broadly and efficiently across a range of genotypes. This study was initiated to identify differential genotype-in vitro protocol responses across a range of bioenergy sorghum parental lines and the common grain sorghum genotype Tx430 in order to characterize response profiles for use in future genetic studies. Two different in vitro protocols, LG and WU, were used for comparisons. Distinct genotype-protocol responses were observed, and the WU protocol performed significantly better for plantlet regeneration. Most bioenergy genotypes performed as well, if not better than Tx430, with Rio and PI329311 as the top regenerating lines. Genotypes displayed protocol-dependent, differential phenolic exudation responses, as indicated by medium browning. During the callus induction phase, genotypes prone to medium browning exhibited a response on WU medium which was either equal or greater than on LG medium. Genotype- and protocol-dependent albino plantlet regeneration was also noted, with three of the bioenergy genotypes showing albino plantlet regeneration. Grassl, Rio and Pink Kafir were susceptible to albino plantlet regeneration, with the response strongly associated with the WU protocol. These bioenergy parental genotypes, and their differential responses under two in vitro protocols, provide tools to further explore and assess the role of genetic loci, candidate genes, and allelic variants in the regulation of in vitro responsiveness in sorghum.
25Sorghum has been considered a recalcitrant plant in vitro, and suffers from a lack of 26 regeneration protocols that function broadly and efficiently across a range of genotypes. This study 27 was initiated to identify differential genotype-in vitro protocol responses across a range of 28 bioenergy sorghum bioenergy parental lines, in order to characterize response profiles for use in 29 future genetic studies. Seven bioenergy sorghum genotypes were compared, along with the 30 common grain sorghum genotype Tx430, for their in vitro regeneration responses using two 31 different in vitro protocols, LG and WU. All genotypes displayed some level of response during 32 in vitro culture with both protocols. Distinct genotype-protocol responses were observed, with the 33 WU protocol significantly better for plantlet regeneration. All bioenergy genotypes, with the 34 exception of Chinese Amber, performed as well, if not better than Tx430, with Rio and PI329311 35 the top regenerating lines. Genotypes displayed protocol-dependent, differential phenolic 36 exudation responses, as indicated by medium browning. During the callus induction phase, 37 genotypes prone to medium browning exhibited a response on WU medium which was either equal 38 or greater than on LG medium, with Pink Kafir and PI329311 the most prone to medium browning. 39 Genotype-and protocol-dependent albino plantlet regeneration was also noted, with three of the 40 bioenergy genotypes showing albino plantlet regeneration. Grassl, Rio and Pink Kafir were 41 susceptible to albino plantlet regeneration, with the response strongly associated with the WU 42 protocol. Pink Kafir displayed the highest albino formation, with close to 25% of regenerating 43 explants forming albino plantlets. 44 45 46 47 48 49 50 51 52 53 Sorghum [Sorghum bicolor (L.) Moench] ranks fifth of the major grain crops in production, 54 area harvested, and yield worldwide (FAOSTAT Database 2017), and more than 300 million 55 people use it as a staple food, particularly in developing semiarid tropical regions (Kebede et al.56
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