Fidelity of sugarcane crosses assessed with SSR markers

Authors: Todd, James; Pan, Yong-Bao; Boykin, Deborah

Submitted to: Agronomy
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/10/2020
Publication Date: 3/12/2020
Citation: Todd, J.R., Pan, Y.-B., Boykin, D.L. 2020. Fidelity of sugarcane crosses assessed with SSR markers. Agronomy. 10(3):1-18. http://doi.org/10.3390/agronomy10030386.
DOI: https://doi.org/10.3390/agronomy10030386

Interpretive Summary: Sugarcane crossing is necessary to develop the new high yielding sugarcane cultivars. Since sugarcane is wind pollinated unintentional and self pollination are possible. These can be controlled by trimming and hot water treating the flowering tassel. Because of this uncertainty it is important to estimate the number of true hybridizations to improve the crossing process. Molecular markers such as Simple Sequence Repeats (SSRs) can be used to determine if appropriate crossing has occurred. If markers from both parents are found in the progeny then it is considered a hybrid. If only the maternal makers are found then it is a self pollination. If markers are found that are not found in either parents the it is the result of contamination an offtype. A sample of 20 seedling from 343 crosses were evaluated with SSR markers and the number of hybrids, selfs and offtypes varied by year. There were significantly lower selfing in those crosses that had selections later in the breeding program. Hot water treatment reduced off-types by 27% and selfing by 20%. This indicated the value in using hot water treatment to reduce unintentional crossing. This research demonstrates the importance of crossing fidelity to reduce selfing which reduces the efficiency of the breeding program.

Technical Abstract: Sugarcane (Saccharum hybrids spp.) is a wind-pollinated species that bears very small yet complete flowers. During crossing, a lack of pollen control (trimming off dehisced florets and hot water treatment) may result in both self-pollination (selfs) and unintentional pollination from stray pollen (off-types). Because of this uncertainty, it is important to estimate the percentage of intentional paternal hybridizations to better understand and possibly improve the crossing process. In this study, six pairs of Simple Sequence Repeats (SSR) primers were used to assess the fidelity of 343 bi-parental crosses made at three U.S. breeding stations in 2002, 2003, 2004, 2005, and 2006. By comparing the SSR fingerprints between the two parents and 20 random progenies, three types of progenies were identified, namely, hybrids, selfs, and off-types. Hybrids have only SSR fingerprints found in either parent; the selfs have SSR fingerprints of the maternal parent; and the off-types have SSR fingerprints that are not found in either parent. The fidelity of the 343 crosses fluctuates from 100% hybrids to 100% off-types. Multinomial analysis indicated that the ratio of hybrids (intentional hybridization) to off-types fluctuated by year and location. Selfing rates (-30.5%) and off-type rates (-9.2%) were lower in crosses that were advanced, but off-type rates were not significant indicating that selfing may reduce advancement rates more than the off-types. Hot water treatment reduced off-types by 27% and selfing by 20%. This research demonstrates the utility of SSR markers for measuring hybridization rates.