SORGHUM-GENSTOCKS

Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population

Genetic Architecture of Chilling Tolerance in Sorghum Dissected with a Nested Association Mapping Population

The Agricultural Research Service (ARS) of the United States of Department of Agriculture (USDA) announces the release of 252 sorghum (Sorghum bicolor L. Moench) mutant lines with available DNA sequence https://www.sorghumbase.org/relnotes. The 252 sorghum mutants were generated using single seed descent, beginning from the wildtype seeds of the inbred line BTx623 (M0) treated with ethyl methane sulfonate (EMS) and concluding at the M3 generation. The M4 seeds were pooled from 10 panicles harvested from the M3 plants and deposited into the mutant library. A core set of 252 lines were selected for whole genome sequencing partly based on specific phenotypes and partly by random selection. This endeavor resulted in detection and cataloguing of more than 1.8 million canonical EMS-induced mutations (or variants). The variants altered the sorghum genome uniformly and bioinformatic analyses indicated that approximately 35,000 genes were affected by large consequential mutations (Jiao et al. 2016).

Description of Methods and Environmental Conditions for Screening of Cold Tolerant Mapping Population

For the cold tolerant population RTx430/PI610727(Gaigaoliang), both cold optimal germinability were assessed under laboratory conditions. Briefly, 25 seeds were sown in polystyrene Petri dishes lined with filter paper moistened with sterile distilled water. Seeds were allowed to incubate/germinate at a constant 12°C (cold germination) or at 30°C (optimal germination) for 8h in the light, in separate controlled temperature chambers and then both treatments were exposed to 20°C for 16h in the dark. Germination under laboratory conditions was determined visually based on protrusion of radicle to approximately 1mm length. Final germination was counted at 4 or 7 days after sowing for optimal and cold temperature test. To determine variation in field emergence, the RILs and parents were sown in 5 x 1 m plots at the USDA-ARS farm in Lubbock, TX (101° 90' west longitude; 33° 59' north latitude) and at Texas Agrilife farm at New Deal, TX (101° 82' west longitude; 33° 69' north latitude). A total of 50 manually selected high quality seeds were sown on top of well prepared beds on April 1, 2009 for both locations. Plots were uniformly irrigated using a drip system after sowing. Seed emergence was measured based on number of seedlings per plot at 14, 21 and 30 days after sowing. The mean field soil and air temperature during the experimental period was 14.9°C and 16.6°C, respectively.

Sorghum genetic stocks hundred seed weights for available inventories updated semi-annually to incorporate new data on current regenerations

Phenotypic evaluation of the original 137 F₂-derived F_6-8 generation inbred lines from the BTx623/IS3620C population was conducted as early as 1994. The population was planted in a randomized complete block design with two replications in College Station, Texas (30.5°N, 96°W) and Lubbock, Texas (33.6°N, 101.9°W). The population was evaluated for 28 traits in both locations and QTL analyses for these traits were performed (Hart et al., 2001; Feltus et al., 2006). In 2004, 119 of the F₇ to F₉ RILs were cultivated and phenotyped in: College Station, Texas (30.5°N, 96°W), Halfway, Texas (34°N, 101.5°W), and Weslaco, Texas (26°N, 98°W). Utilizing these 119 F₇ to F₉ RILs, 15 agronomic traits including primary, secondary, and tertiary branching were measured and QTL analyses for these traits were performed by Brown et al. (2006). Laboratory studies were also conducted on a subset of the population at the USDA-ARS Plant Stress & Germplasm Development Unit in Lubbock, TX in 2004 and 2005 for seedling tolerance to chilling and high temperatures.

Additional information about the population can be viewed at RIL BTx623 x IS3620C.

In early spring of 2011, the BTx623HKZ_recombinant inbred mapping population including the two parents and 8 commercial checks were planted in replicated plots in three locations representing the US sorghum belt temperate region, USDA zones 4b to 6b between April 1 and 18 (differing due to latitudes of location and precipitation) to evaluate variation for early season field traits for cold tolerance based on field emergence and seedling vigor, biomass. The locations used for field testing were; Lubbock, Texas (33.6°N -101.88°W, 2381 ft. elevation), Manhattan, Kansas (39.21°N -96.51°W, 1053 ft. elevation) and Wall, South Dakota (43.99°N -102.24°W, 2208 ft. elevation). The mean ambient and soil temperatures for all three locations at the time of planting were: Lubbock, TX- 18.3; 17.7 °C; Manhattan, KS- 12.2; 14.4°C; Wall, SD- 12.6; 12.5°C. Each entry was planted in 10 m long plots with 100 cm spacing between plots and equal number of seeds were planted per plot. Field emergence was evaluated on a weekly basis and at 30 days after planting as % field emergence. Seedling vigor was rated on a 1-5 scale, with rating of 1 as robust vigor and 5 as poor vigor. Subsequently, five seedlings in the inner section of each plot were harvested for above ground biomass to determine dry weight.

The parents of the population, BTx623_ is a combine type elite line that germinates poorly during early cool season of the year and Niu Sheng Zui (PI 568016) is a Chinese landrace that exhibit >70% germination under cool conditions in temperate regions of the US sorghum belt (USDA hardiness zones 4b to 6b). The BTx623NSZ_Recombinant Inbred Mapping Population (RIMP) was developed by hand emasculation of the female parent BTx623 and pollination with pollen from. The resulting F1 hybrid was intermediate in height, with brown seed color. A total of 300 F2 plants were planted, but only 292 lines were advanced single seed descent breeding technique in Lubbock, Texas from F3 to F4 generations. From F5 to F7, seeds were produced alternately between Lubbock, Texas and Puerto Rico. At the F6:7 stage of development ten representative uniform plants were tagged and seeds were bulked from the 10 tagged plants to compose each line. A total of 292 RILs were generated and are used to represent the BTx623NSZ_RIMP. In spring of 2015 through 2017, the BTx623NSZ_RIMP including the two parents and 8 commercial checks were planted in replicated plots in three locations representing the US sorghum belt temperate region, USDA zones 4b to 6b between April 1 and 18 (differing due to latitudes of location and precipitation) to evaluate variation for early season field traits for cold tolerance based on field emergence and seedling vigor, biomass. The locations used for field testing were; Lubbock, Texas (33.6°N -101.88°W, 2381 ft. elevation and Manhattan, Kansas (39.21°N -96.51°W, 1053 ft. elevation). The mean ambient and soil temperatures for all three locations at the time of planting were: Lubbock, TX- 18.3; 17.7 °C; Manhattan, KS- 12.2; 14.4°C; Wall, SD- 12.6; 12.5°C. Each entry was planted in 10 m long plots with 100 cm spacing between plots and equal number of seeds were planted per plot. Field emergence was evaluated on a weekly basis and at 30 days after planting as % field emergence. Seedling vigor was rated on a 1-5 scale, with rating of 1 as robust vigor and 5 as poor vigor. Subsequently, five seedlings in the inner section of each plot were harvested for above ground biomass to determine dry weight.

The Kansas State University announces the release of a nested association mapping population (NAM) with a total of 2,133 recombinant inbred lines (RILs) developed from ten bi-parental sub-populations. These 2,133 RILs were derived from 10 diversified founder lines each crossed separately to RTx430 to develop ten bi-parental mapping sub-populations and released by the Kansas State University (KS) in July 2019. Extensive field studies on the founder lines having wide genetic and geographical diversity simply proved the unique and distinguishable nature of the developed KS-RTx430NAM population for the traits related to biotic and abiotic stresses. The population is currently in F9 and reached the maximum homozygosity with genetic purity and uniformity with each RIL. All RILs have been genotyped through genotype-by-sequencing (GBS) using an illumina HISeq 2500 with a high-output flowcell and 100-cycle single-end sequencing. KS-RTx430NAM will serve as a new genetic resource and for research and developmental purpose for the exploitation of wide genetic diversity of many complex yield traits.

The Kansas State University announces the release of a nested association mapping population (NAM) with a total of 2,133 recombinant inbred lines (RILs) developed from ten bi-parental sub-populations. These 2,133 RILs were derived from 10 diversified founder lines each crossed separately to RTx430 to develop ten bi-parental mapping sub-populations and released by the Kansas State University (KS) in July 2019. Extensive field studies on the founder lines having wide genetic and geographical diversity simply proved the unique and distinguishable nature of the developed KS-RTx430NAM population for the traits related to biotic and abiotic stresses. The population is currently in F9 and reached the maximum homozygosity with genetic purity and uniformity with each RIL. All RILs have been genotyped through genotype-by-sequencing (GBS) using an illumina HISeq 2500 with a high-output flowcell and 100-cycle single-end sequencing. KS-RTx430NAM will serve as a new genetic resource and for research and developmental purpose for the exploitation of wide genetic diversity of many complex yield traits.

The Kansas State University announces the release of a nested association mapping population (NAM) with a total of 2,133 recombinant inbred lines (RILs) developed from ten bi-parental sub-populations. These 2,133 RILs were derived from 10 diversified founder lines each crossed separately to RTx430 to develop ten bi-parental mapping sub-populations and released by the Kansas State University (KS) in July 2019. Extensive field studies on the founder lines having wide genetic and geographical diversity simply proved the unique and distinguishable nature of the developed KS-RTx430NAM population for the traits related to biotic and abiotic stresses. The population is currently in F9 and reached the maximum homozygosity with genetic purity and uniformity with each RIL. All RILs have been genotyped through genotype-by-sequencing (GBS) using an illumina HISeq 2500 with a high-output flowcell and 100-cycle single-end sequencing. KS-RTx430NAM will serve as a new genetic resource and for research and developmental purpose for the exploitation of wide genetic diversity of many complex yield traits.

The Kansas State University announces the release of a nested association mapping population (NAM) with a total of 2,133 recombinant inbred lines (RILs) developed from ten bi-parental sub-populations. These 2,133 RILs were derived from 10 diversified founder lines each crossed separately to RTx430 to develop ten bi-parental mapping sub-populations and released by the Kansas State University (KS) in July 2019. Extensive field studies on the founder lines having wide genetic and geographical diversity simply proved the unique and distinguishable nature of the developed KS-RTx430NAM population for the traits related to biotic and abiotic stresses. The population is currently in F9 and reached the maximum homozygosity with genetic purity and uniformity with each RIL. All RILs have been genotyped through genotype-by-sequencing (GBS) using an illumina HISeq 2500 with a high-output flowcell and 100-cycle single-end sequencing. KS-RTx430NAM will serve as a new genetic resource and for research and developmental purpose for the exploitation of wide genetic diversity of many complex yield traits.

The Kansas State University announces the release of a nested association mapping population (NAM) with a total of 2,133 recombinant inbred lines (RILs) developed from ten bi-parental sub-populations. These 2,133 RILs were derived from 10 diversified founder lines each crossed separately to RTx430 to develop ten bi-parental mapping sub-populations and released by the Kansas State University (KS) in July 2019. Extensive field studies on the founder lines having wide genetic and geographical diversity simply proved the unique and distinguishable nature of the developed KS-RTx430NAM population for the traits related to biotic and abiotic stresses. The population is currently in F9 and reached the maximum homozygosity with genetic purity and uniformity with each RIL. All RILs have been genotyped through genotype-by-sequencing (GBS) using an illumina HISeq 2500 with a high-output flowcell and 100-cycle single-end sequencing. KS-RTx430NAM will serve as a new genetic resource and for research and developmental purpose for the exploitation of wide genetic diversity of many complex yield traits.

The Kansas State University announces the release of a nested association mapping population (NAM) with a total of 2,133 recombinant inbred lines (RILs) developed from ten bi-parental sub-populations. These 2,133 RILs were derived from 10 diversified founder lines each crossed separately to RTx430 to develop ten bi-parental mapping sub-populations and released by the Kansas State University (KS) in July 2019. Extensive field studies on the founder lines having wide genetic and geographical diversity simply proved the unique and distinguishable nature of the developed KS-RTx430NAM population for the traits related to biotic and abiotic stresses. The population is currently in F9 and reached the maximum homozygosity with genetic purity and uniformity with each RIL. All RILs have been genotyped through genotype-by-sequencing (GBS) using an illumina HISeq 2500 with a high-output flowcell and 100-cycle single-end sequencing. KS-RTx430NAM will serve as a new genetic resource and for research and developmental purpose for the exploitation of wide genetic diversity of many complex yield traits.

The Kansas State University announces the release of a nested association mapping population (NAM) with a total of 2,133 recombinant inbred lines (RILs) developed from ten bi-parental sub-populations. These 2,133 RILs were derived from 10 diversified founder lines each crossed separately to RTx430 to develop ten bi-parental mapping sub-populations and released by the Kansas State University (KS) in July 2019. Extensive field studies on the founder lines having wide genetic and geographical diversity simply proved the unique and distinguishable nature of the developed KS-RTx430NAM population for the traits related to biotic and abiotic stresses. The population is currently in F9 and reached the maximum homozygosity with genetic purity and uniformity with each RIL. All RILs have been genotyped through genotype-by-sequencing (GBS) using an illumina HISeq 2500 with a high-output flowcell and 100-cycle single-end sequencing. KS-RTx430NAM will serve as a new genetic resource and for research and developmental purpose for the exploitation of wide genetic diversity of many complex yield traits.

The Kansas State University announces the release of a nested association mapping population (NAM) with a total of 2,133 recombinant inbred lines (RILs) developed from ten bi-parental sub-populations. These 2,133 RILs were derived from 10 diversified founder lines each crossed separately to RTx430 to develop ten bi-parental mapping sub-populations and released by the Kansas State University (KS) in July 2019. Extensive field studies on the founder lines having wide genetic and geographical diversity simply proved the unique and distinguishable nature of the developed KS-RTx430NAM population for the traits related to biotic and abiotic stresses. The population is currently in F9 and reached the maximum homozygosity with genetic purity and uniformity with each RIL. All RILs have been genotyped through genotype-by-sequencing (GBS) using an illumina HISeq 2500 with a high-output flowcell and 100-cycle single-end sequencing. KS-RTx430NAM will serve as a new genetic resource and for research and developmental purpose for the exploitation of wide genetic diversity of many complex yield traits.

The Kansas State University announces the release of a nested association mapping population (NAM) with a total of 2,133 recombinant inbred lines (RILs) developed from ten bi-parental sub-populations. These 2,133 RILs were derived from 10 diversified founder lines each crossed separately to RTx430 to develop ten bi-parental mapping sub-populations and released by the Kansas State University (KS) in July 2019. Extensive field studies on the founder lines having wide genetic and geographical diversity simply proved the unique and distinguishable nature of the developed KS-RTx430NAM population for the traits related to biotic and abiotic stresses. The population is currently in F9 and reached the maximum homozygosity with genetic purity and uniformity with each RIL. All RILs have been genotyped through genotype-by-sequencing (GBS) using an illumina HISeq 2500 with a high-output flowcell and 100-cycle single-end sequencing. KS-RTx430NAM will serve as a new genetic resource and for research and developmental purpose for the exploitation of wide genetic diversity of many complex yield traits.

The Kansas State University announces the release of a nested association mapping population (NAM) with a total of 2,133 recombinant inbred lines (RILs) developed from ten bi-parental sub-populations. These 2,133 RILs were derived from 10 diversified founder lines each crossed separately to RTx430 to develop ten bi-parental mapping sub-populations and released by the Kansas State University (KS) in July 2019. Extensive field studies on the founder lines having wide genetic and geographical diversity simply proved the unique and distinguishable nature of the developed KS-RTx430NAM population for the traits related to biotic and abiotic stresses. The population is currently in F9 and reached the maximum homozygosity with genetic purity and uniformity with each RIL. All RILs have been genotyped through genotype-by-sequencing (GBS) using an illumina HISeq 2500 with a high-output flowcell and 100-cycle single-end sequencing. KS-RTx430NAM will serve as a new genetic resource and for research and developmental purpose for the exploitation of wide genetic diversity of many complex yield traits.

The late Keith Schertz, USDA, ARS collected 536 sorghum lines consisting of natural and induced mutants, linkage analysis lines, and chromosome translocation lines from various sources around the world. In order to make this mutant collection available for sorghum genetic and genomic studies, the seed inventories were categorized, replanted, and phenotypes confirmed based on Dr. Schertz's orignal notes. Seeds were replanted at Halfway, Texas in 2004, and at Lubbock, Texas in 2006 and 2009. Standard cultivation practices were followed and irrigation was applied as needed. Phenotyping was conducted several times during the growing season at seedling, vegetative, reproductive, and maturity stages. Days to flowering, plant height, and exsertion were recorded.