Genetic Architecture Of Domestication-Related Traits In Sorghum

Crop domestication dates from Neolithic Revolution, occurred in 12000 years ago. Since then, a variety of crops have been domesticated from their wild progenitors independently in different continents. As the fifth major crop, sorghum [Sorghum bicolor (L.) Moench.] originated from Sudan, Ethiopia and the surrounding areas of Northeast Africa. During the process of domestication, enormous morphological and physiological traits have been reshaped, which include the reduced grain shattering, lightened hull and grain color, synchronized flowering time and grain maturation, increased seed size as well as more compact plant architecture. Here, using the F2 and F2:3 populations derived from a cross between the cultivated sorghum Tx623 and a wild species SV, QTLs for domestication-related traits were detected, and the major locus on chromosome 10 for heading date as well as the two loci for plant height on chromosome 9 and 1 were fine-mapped, then the role of the candidate genes played in the sorghum domestication were analyzed.The major results are as follows:1.272 F2 individuals were assayed with 216 SSR markers evenly distributed on the total 10 chromosomes, to construct the genetic linkage map by R/qtl package. The overall map spanned 1610.5 cM, and the average length of every two neighboring markers reached 7.8 cM.2. The 18 domesticated traits of F2 population (Beijing) and the 6 traits of F2:3 population (Hainan) were investigated. A total of 66 QTLs were identified by R/qtl, which distributed across 10 chromosomes. However, its distribution was not even, some QTLs tended to concentrated presence. The positive effects of QTLs from the cultivar Tx623 were favorable for leaf length, leaf width, grain weight and grain width, while positive effects from wild parent species were favorable for plant height and tillering.3. According to the QTL mapping results of F2 population and F2:3 population, the major QTL controlling heading date on chromosome 10 was identified. With the method of recombinant-derived progeny verification through marker test, the loci were fine-mapped and narrowed down within a 37-kb genomic segment. In this region, a gene sb10g010050 encodes a CONSTANS-like protein, which corresponds to rice heading date gene HD1. The deletion of 5-bp in the first exon of SV allele leads to the loss of the zinc finger and the CCT domain, resulting in the loss of function. Nucleotide diversity apparently decreased in domesticated sorghum than that in wild sorghum and Tajima’s D test showed a slight significant selection sweep was still detected at the site of the 5-bp deletion (Tajima D’s test= 2.39, P<0.05). Comparative mapping identified a syntenic block corresponding to the HD1 locus, containing four highly conserved chromosomal segments on sorghum chromosome 10, maize chromosome 9, rice chromosome 6 and foxtail millet chromosome 4, respectively. And major QTLs for flowering time had been placed within the syntenic block on rice chromosome 6 and foxtail millet chromosome 4. A large DNA sequence analysis of HD1 orthologs in foxtail millet revealed a splicing variant from "GT" to "AT" was common (78/98), this variant resulted in a splicing site shift from GT at 787bp to GT at 754bp. Association testing detected the most significant (P=9.50×10-5) was present at the splicing variant site. Nucleotide diversity within the gene was decreased markedly in domesticated foxtail millet, compared with wild foxtail millet. All above results suggest that HD1 gene of sorghum, rice and foxtail millet was under parallel domestication.4. Based on the F2 and F2:3 QTL mapping results, a major QTL(dwl) contributing to plant height and other traits on chromosome 9 were detected. With a sequential QTL fine-mapping strategy using recombinant-derived progeny, we finally narrowed down the locus within 13.98-kb. Sequencing of the gene Sobic.009G229800 in this interval revealed the only one variant from A to T in the second exon, leading to premature termination in Tx623 allele. A large DNA sequence analysis of candidate gene showed premature termination was common in cultivated sorghum from the United States and India, and the dwl gene sequences of such these dwarf varieties have no nucleotide difference, indicating that this premature termination mutation took place not a long time ago. DNA diversity of cultivated sorghum without the causal change showed no significant decrease compared with the wide line, suggesting dwl gene was not selected during domestication. Thus this mutation was created through modern breeding.5. The QTL-phl for plant height on chromosome 1 was fine-mapped and the interval was narrowed down into 24.5-kb. Only one gene, Sobic.001G106000, which encoded a KNOTTED-like transcription factor, was found in the interval. Sequencing of the two parent lines found two SNP mutations which could cause amino acid sequence change, however, it might not be the reason of phenotypic variation.