b'PARTNER CONTENTNew Mid-Density SNP Panel Developed for U.S. RiceBy: Beni KaufmannA ccording to the US Department of Agriculture, Americanand genome wide markers commonly used in US rice germplasm. farmers in 2021 harvested nearly 2.5 million acres of long-The panel will be useful for genomic selection, marker-assisted and medium-grain rice, averaging 7,709 pounds/acre. Thatbackcrossing, QTL mapping, trait profiling, and seed purity and yield, which was up over 90 lbs/ac compared to 2020, was thehybridity testing. highest yield on record: a gain directly attributable to rice breed- The LSU500 SNP rice panel was made possible by the combined ing efforts. Given that rice is the single most important food cropefforts of LSU and Cornell University researchers and the multi-on Earth, providing more than 20% of all calories consumed byplexing capacity of AgriPlex Genomics PlexSeq platform. PlexSeq humans worldwide, breeding even higher yielding, more nutri- saves critical time and expenses thanks to multiple efficiencies:tious rice is critical. Thanks to the introduction of LSU500, aPlexSeq offers the PlexForm artificial intelligence multiplexing new mid-density single nucleotide polymorphic (SNP) panel foralgorithm, which can design all possible primers around any SNP rice developed by Louisiana State University (LSU) and Cornellof interest and identify optimal sets of primers that can be mixed University and made possible through Agriplex Genomics mid- in just one PCR amplification reaction. Once the amplifications density multiplexing technology, faster, more cost-efficient riceare complete, the amplicon libraries produced from each sample breeding gains will be possible ahead.are equivalent in concentration and do not require any additional Modern molecular breeding practices depend on establishingequalization steps. A mixture of all the libraries is subjected to one suitable DNA marker sets for accurate, early selection of individu- bead clean-up and is then loaded onto the sequencer. The PlexSeq als of interest. These marker sets shorten the number of selec- process requires minute quantities of crude DNA isolatable from a tion cycles required, reduce new lines time to market, and lowervariety of tissues. The process is amenable to automation; all steps overall breeding costs. While high-density arrays that interrogatecan be conducted on liquid handlers and high-capacity thermocy-many SNPs per DNA sample have been available for some time,clers, enabling high throughput genotyping. AgriPlex Genomics its only recently that breeders have benefited from new high- vast collection of barcode combinations permits simultaneous throughput, cost-effective mid-density genotyping solutions. Forsequencing limited only by the sequencers capacity. rice breeders, the IRRI 1k Rice Custom Amplicon (RiCA) panelBecause the panel is a collection of PCR primers untethered to was introduced as a breeding tool mostly for long grain rice (Ory- a surface, the markers in the panel are dynamically alterable and za sativa indica). Now, the newly developed LSU500 SNP geneticcustomizable. The LSU500 SNP rice panel is designed to be dynam-panel is adding a mid-density genotyping tool for the short grain,ic, with its genomic screen and trait markers periodically updated sticky rice (Oryza sativa japonica) breeders.to maximize relevance and optimize its various applications.The LSU500 panel is mostly derived from the C7AIR Rice 7K SNP array (Morales et al., 2020). SNPs that were polymorphic in 74 tropical Oryza japonica varieties and well distributed along the genome were selected. Initially, 2086 SNPs were identified. That number was further reduced to the final 500 SNPs panel to minimize costs for routine genotyping (without signifi-cantly decreasing the panels ability to capture the ge-netic variation of the target germplasm), and to enable the panel to be used for genomic selection within the Southern U.S. rice O. japonica breeding germplasm. After filtering, haplotype blocks were identified representing groups of SNPs with alleles that are co-inherited due to linkage, and the minimum number of SNP markers needed to uniquely identify each haplotype block were selected (average distance between markers = 663.1 kb). The panel was augmented with trait associated INTERNATIONAL EDITION 2022SEEDWORLD.COM /59'