Utilization of a sugarcane100K single nucleotide polymorphisms microarray-derived high-density genetic map in quantitative trait loci mapping and function role prediction of genes related to chlorophyll content in sugarcane

Authors: LU, GUILONG - Fujian Agricultural & Forestry University; Pan, Yong-Bao; WANG, ZHOUTAO - Fujian Agricultural & Forestry University; XU, FU - Fujian Agricultural & Forestry University; CHENG, WEI - Fujian Agricultural & Forestry University; HUANG, XINGE - Fujian Agricultural & Forestry University; REN, HUI - Fujian Agricultural & Forestry University; PANG, CHAO - Fujian Agricultural & Forestry University; QUE, YOUXIONG - Fujian Agricultural & Forestry University; XU, LIPING - Fujian Agricultural & Forestry University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/30/2021
Publication Date: 12/28/2021
Citation: Lu, G., Pan, Y., Wang, Z., Xu, F., Cheng, W., Huang, X., Ren, H., Pang, C., Que, Y., Xu, L. 2021. Utilization of a sugarcane100K single nucleotide polymorphisms microarray-derived high-density genetic map in quantitative trait loci mapping and function role prediction of genes related to chlorophyll content in sugarcane. Frontiers in Plant Science. 12. Article 817875. https://doi.org/10.3389/fpls.2021.817875.
DOI: https://doi.org/10.3389/fpls.2021.817875

Interpretive Summary: Chlorophyll is the most important pigment for plant photosynthesis that plays an important role in plant growth and crop production. In this study, the chlorophyll content trait was explored to improve sugarcane yield. Two hundred and eighty-five offsprings from the cross YT93-159 × ROC22 were included as the experiment materials. During the elongation stage, the chlorophyll content of the topmost fully extended leaves was measured using a SPAD-502 meter. The measurements were conducted for three years on plant cane, first ratoon, and second ratoon crop sesons. The data were subjet to linkage analysis using a high-density genetic map, which was constructed based on a published sugarcane 100K SNP chip. In addition, data on Fv/Fm, plant height, stalk diameter, and Brix were also collected from the plant cane crop during the elongation and maturation stages. The results showed that the SPAD values were significantly and positively correlated with the Fv/Fm data from elongation stage and with the plant height, stalk diameter, and Brix data from maturity stage. Therefore, the SPAD value can be used as a reference to predict the growth potential of sugarcane. In addition, 27 QTL markers were detected, of which a major QTL qCC-R1 accounted for 13% of phenotypic variations and the other 26 minor QTLs explained 2.37%-7.99% phenotypic variations. Lastly, 20 candidate genes for chlorophyll content were identified within a 200,000-base pairs extension region on either side of the27 QTL markers. Four genes were involved in chlorophyll synthesis and 16 were involved in chlorophyll catabolic pathway, chloroplast organization, or photosynthesis. These results provide a theoretical reference for analyzing the genetic mechanism of chlorophyll synthesis and subsequent improvement of photosynthetic characteristics in sugarcane.

Technical Abstract: Chlorophyll is the most important pigment for plant photosynthesis that plays an important role in crop growth and production. In this study, the chlorophyll content trait was explored to improve sugarcane yield. Two hundred and eighty-five F1 progenies from the cross YT93-159 × ROC22 with significantly different chlorophyll contents were included as test materials. The chlorophyll content of the +1 leaves during elongation phase was measured using a SPAD-502 meter through a three-crop cycle (plant cane, first ratoon, and second ratoon). Linkage analysis was conducted on a high-density genetic map constructed based on the sugarcane 100K SNP chip. In addition, Fv/Fm, plant height, stalk diameter, Brix data were collected on plant cane during the elongation and maturation phases. The results showed that the +1 leaf SPAD values were significantly and positively correlated with the Fv/Fm during elongation phase, as well as with plant height, stem diameter, and brix during maturity phase (P<0.01). Therefore, the +1 leaf SPAD value can be used as an important reference to evaluate the growth potential of sugarcane. The broad sense heritability (H2) of the chlorophyll content trait was 0.66 for plant cane crop, 0.67 for first ratoon crop, and 0.73 for second ratoon crop, respectively, indicating that this trait was mainly controlled by genetic factors. Twenty-seven quantitative trait loci (QTL) were detected by QTL mapping. Among them, a major QTL, qCC-R1, could account for 12.95% of phenotypic variation explained (PVE), and the other 26 were minor QTLs explaining for 2.37%-7.99% PVE. Twenty related candidate genes were identified in a 200-Kb extension region based on the above QTL intervals, of which four were homologous genes in the chlorophyll synthesis process and 16 played a certain role in chlorophyll catabolic pathway, chloroplast organization, or photosynthesis. These results provide a theoretical reference for analyzing the genetic mechanism of chlorophyll synthesis and subsequent improvement of photosynthetic characteristics in sugarcane.