Introduction

Rice (Oryza Sativa) is the most important food crop for human nutrition and caloric intake, providing more than 20% of the calories consumed by humans worldwide. Rice is a key agricultural commodity, being the third most produced crop worldwide.


Oryza sativa is a monocot of the family Poaceae (grasses) and contains two major subspecies: long-grained indica rice variety and the sticky, short-grained japonica or sinica variety. Oryza sativa japonica was first domesticated in the Yangtze River basin in China 13,500 to 8,200 years ago, while O. sativa indica was domesticated around the Ganges River in India 8,500 to 4,500 years ago.

US Rice

Rice has been grown in the US since the mid-19th century. U.S. rice farming started in South Carolina and Georgia where rice plantations were built on rice cultivation culture brought Western African slaves. After the Civil War, the southeastern rice culture became less profitable and almost disappeared. Further west in southern Arkansas, Louisiana, and east Texas, still in the 19th century, many farmers grew rice in wet marshes and low-lying prairies where they could also farm crawfish when the fields were flooded.


Presently US rice is grown in Arkansas, Mississippi, Missouri, Louisiana, Texas, and California. The southern states grow predominately long-grain types, whereas California grows mostly medium-grain types. Three states—Arkansas, California, and Louisiana—collectively account for approximately 82% of U.S. production. The majority of domestic utilization of U.S. rice is purposed for direct food consumption (58%), 16% is used for processed foods and 16% for brewing beer. The remaining 10% is found in pet food.


The U.S. Department of Agriculture’s National Agricultural Statistics Service reported that the year-end production estimate of 2021 was 191.8 million hundredweight (cwt, 1cwt = 45.3592 kg in the US) and the total harvested area was 2.49 million acres. These values are slightly lower from previous years, which is mostly attributed to lower land usage. However, the average yield in the US was 7,709 pounds/acre, being 90 pounds above the previous year and the highest yield on record.

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The top yield of the US rice sector can be credited to recent achievements in rice breeding. These modern breeding practices are dependent on establishing a suitable marker set a reliable, and effective genotyping platforms capable of providing informative marker data with fast turnaround time and low cost.


Table 1: Rice Area Planted and Harvested, Yield, and Production by Class – States and United States: 2021 (Adapted from U.S. Department of Agriculture’s National Agricultural Statistics Service (NASS), January 2022, Crop Production 2021 Summary); NA – No data available, ctw: Hundred weight


The LSU 500 SNP Panel

The Louisiana State University (LSU) 500 SNP Panel was developed by Chris Hernandez (Postdoctoral Associate) and Tommaso Cerioli (Ph.D. Student) in the laboratories of Prof. Adam Famoso at the Louisiana State University AgCetner and Prof. Kelly Robbins at Cornell University.


The 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; this SNP selection was taken through two cycles of reduction (Figure 1) that lead to the final 500 SNPs panel. The goal of the reduction was to reduce the size of the marker set to minimize costs for routine genotyping, without significantly decreasing the ability to capture the genetic variation of the target germplasm, and to enable the use of the panel for Genomic Selection implementation within Southern U.S. rice breeding germplasm.


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Figure 1: Marker density across different marker sets. A) C7AIR rice SNP array (7K) marker density; B) 7K filtered with MAF >0.1 and missing data <20% marker density; C) LSU1200 marker density; D) LSU500 marker density. From Cerioli et al., 2022.


The reduction process involved filtering markers that demonstrated genotyping success rate higher than 80% (less than 20% missing data), and a minor allele frequency (MAF) greater than 0.1 (average MAF among a geographical diversity set of rice lines = 0.22).
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 and genome wide markers commonly used in US rice germplasm.