Bringing high-throughput techniques to orphan crop of Africa: Highlights from the Tef TILLING Project

Orphan- or understudied-crops are mostly staple food crops in developing world. They are broadly classified under cereals, legumes, root crops, fruits and vegetables. These under-researched crops contribute to the diet of a large portion of resource-poor consumers and at the same time generate income for small-holder farmers in developing countries, particularly in Africa. In addition, they perform better than major crops of the world under extreme soil and climatic conditions. However, orphan crops are not without problems. Due to lack of scientific investigation, most of them produce low yields while others have a variety of toxins that affect the health of consumers. Here, we present some highlights on the status and future perspectives of the Tef Biotechnology Project that employs modern improvement technique in order to genetically improve tef (Eragrostis tef), one of the most important orphan crop in Africa. A reverse genetics approach known as TILLING (Targeting Induced Local Lesions IN Genome) is implemented in order to tackle lodging, the major yield limiting factor in tef.Key words: Orphan crops, underresearched crops, Eragrostis tef, TILLING, semi-dwarf.

Forage-Based Beef Production Research at the Armstrong Outlying Research Farm

Fifty-five yearling crossbred steers and 3C cow-calf pairs were used in a forage-based beef production system demonstration project at the Armstrong Outlying Research Farm. From May 11 to June 13, steers rotationally grazed a 41-acre grass pasture that was divided into eight paddocks. From June 13 to August 24, steers were placed in a drylot and fed berseem clover/oat soilage from a strip-intercropping system. Beginning June 5, 36 cow-calf pairs were allowed to rotationally graze the 41-acre pasture until September 18. Calf weight gains for the 110 days were 1.57 pounds per day, and total production from the pasture was 151 pounds per acre. No cow weight change or condition score change was measured. Total steer production was 29 and 580 pounds per acre or average daily gains were .67 and 2.23 pounds while grazing pasture and being fed in a drylot.

Effects of Pasture Conditions in Spring on Seasonal Forage Productivity

Fifteen beef cow-calf producers in southern Iowa were selected based on locality, management level, historical date of grazing initiation and desire to participate in the project. In 1997 and 1998, all producers kept records of production and economic data using the Integrated Resource Management-Standardized Performance Analysis (IRM-SPA) records program. At the initiation of grazing on each farm in 1997 and 1998, Julian date, degree-days, cumulative precipitation, and soil moisture, phosphorus, and potassium concentrations were determined. Also determined were pH, temperature, and load-bearing capacity; and forage mass, sward height, morphology and dry matter concentration. Over the grazing season, forage production, measured both by cumulative mass and sward height, forage in vitro digestible dry matter concentration, and crude protein concentration were determined monthly. In the fall of 1996 the primary species in pastures on farms used in this project were cool-season grasses, which composed 76% of the live forage whereas legumes and weeds composed 8.3 and 15.3%, respectively. The average number of paddocks was 4.1, reflecting a low intensity rotational stocking system on most farms. The average dates of grazing initiation were May 5 and April 29 in 1997 and 1998, respectively, with standard deviations of 14.8 and 14.1 days. Because the average soil moisture of 23% was dry and did not differ between years, it seems that most producers delayed the initiation of grazing to avoid muddy conditions by initiating grazing at a nearly equal soil moisture. However, Julian date, degree-days, soil temperature and morphology index at grazing initiation were negatively related to seasonal forage production, measured as mass or sward height, in 1998. And forage mass and height at grazing initiation were negatively related to seasonal forage production, measured as sward height, in 1997. Moreover, the concentrations of digestible dry matter at the initiation of and during the grazing season and the concentrations of crude protein during the grazing season were lower than desired for optimal animal performance. Because the mean seasonal digestible dry matter concentration was negatively related to initial forage mass in 1997 and mean seasonal crude proteins concentrations were negatively related to the Julian date, degree-days, and morphology indeces in both years, it seems that delaying the initiation of grazing until pasture soils are not muddy, is limiting the quality as well as the quantity of pasture forage. In 1997, forage production and digestibility were positively related to the soil phosphorus concentration. Soil potassium concentration was positively related to forage digestibility in 1997 and forage production and crude protein concentration in 1998. Increasing the number of paddocks increased forage production, measured as sward height, in 1997, and forage digestible dry matter concentration in 1998. Increasing yields or the concentrations of digestible dry matter or crude protein of pasture forage reduced the costs of purchased feed per cow.

A Survey of Forage Quality Following a Flood Year: 1994

A team of extension livestock specialists and county extension workers collected 362 forage samples from cooperating producers in 55 Iowa Counties. Summaries of the three forage types showed normal feed analysis for energy and protein. Micro minerals were also analyzed with 11% of samples being below National Research Council 1984 selenium and zinc requirements for beef.

Pasture Conditions at the Initiation of Grazing to Optimize Forage Productivity: A Progress Report

To determine environmental, soil, and sward effects at the initiation of cattle grazing in the spring on seasonal (forage accumulated during the grazing season) and cumulative (seasonal + initial forage mass) forage accumulation (FA), 15 commercial cow-calf producers from southern Iowa were selected by historical initial grazing date. At grazing initiation, twelve .25-m2 samples were hand-clipped from each pasture and sward heights (SH) measured with a falling plane meter (4.8 kg/m2) to determine initial forage mass. At each location, soil temperature and load bearing capacity (LBC) were measured and a soil sample was collected to measure pH and moisture, P, and K concentrations. Cumulative degree-days (base=3.85°C) and precipitation at grazing initiation were calculated from NOAA records. At the beginning of each month, at least three grazing exclosures were placed on each grazed pasture to determine monthly FA. SH in each exclosure was recorded, and a .25-m2 forage sample was hand-clipped proximate to each exclosure. At the end of each month, SH was recorded and .25-m2 hand-clipped forage samples from inside exclosures were obtained. In linear regressions, cumulative and seasonal SH increased with greater soil P (r2=.5049 and .5417), soil K (r2=.4675 and .4397), and initial forage mass (r2=.1984 and .2801). Seasonal SH increased with earlier initial grazing dates (r2=.1996) and less accumulated degree-days (r2=.2364). Cumulative and seasonal FA increased with earlier initial grazing dates (r2=.2106 and .3744), lower soil temperatures (r2=.2617 and.2874), and greater soil P (r2=.3489 and .2598). Cumulative FA increased with greater soil K (r2=.4675). In quadratic regressions, cumulative and seasonal SH were correlated to soil P (r2=.6310 and .5310) and soil K (r2=.5095 and.4401). Cumulative and seasonal FA were correlated to degree days (r2=.3630 and.4013) and initial grazing date (r2=.3425 and .4088). Cumulative FA was correlated to soil P (r2=.3539), and seasonal FA was correlated to soil moisture (r2=.3688).

Integrating the Use of Spring- and Fall-Calving Beef Cows in a Year-round Grazing System (A Progress Report)

Animal production, hay production and feeding, and the yields and composition of forage from summer and winter grass-legume pastures and winter corn crop residue fields from a year-round grazing system were compared with those of a conventional system. The year-round grazing system utilized 1.67 acres of smooth bromegrass-orchardgrass-birdsfoot trefoil pasture per cow in the summer, and 1.25 acres of stockpiled tall fescue-red clover pasture per cow, 1.25 acres of stockpiled smooth bromegrass-red clover pasture per cow, and 1.25 acres of corn crop residues per cow during winter for spring- and fall-calving cows and stockers. First-cutting hay was harvested from the tall fescue-red clover and smooth bromegrass-red clover pastures to meet supplemental needs of cows and calves during winter. In the conventional system (called the minimal land system), spring-calving cows grazed smooth bromegrass-orchardgrass-birdsfoot trefoil pastures at 3.33 acres/cow during summer with first cutting hay removed from one-half of these acres. This hay was fed to these cows in a drylot during winter. All summer grazing was done by rotational stocking for both systems, and winter grazing of the corn crop residues and stockpiled forages for pregnant spring-calving cows and lactating fall-calving cows in the year-round system was managed by strip-stocking. Hay was fed to springcalving cows in both systems to maintain a mean body condition score of 5 on a 9-point scale, but was fed to fall-calving cows to maintain a mean body condition score of greater than 3. Over winter, fall-calving cows lost more body weight and condition than spring calving cows, but there were no differences in body weight or condition score change between spring-calving cows in either system. Fall- and spring-calving cows in the yearround grazing system required 934 and 1,395 lb. hay dry matter/cow for maintenance during the winter whereas spring-calving cows in drylot required 4,776 lb. hay dry matter/cow. Rebreeding rates were not affected by management system. Average daily gains of spring-born calves did not differ between systems, but were greater than fall calves. Because of differences in land areas for the two systems, weight production of calves per acre of cows in the minimal land system was greater than those of the year-round grazing system, but when the additional weight gains of the stocker cattle were considered, production of total growing animals did not differ between the two systems.

Efficacy of Grazing Stockpiled Perennial Forages for Winter Maintenance of Beef Cows

In a three year study, wintering systems utilizing the grazing of stockpiled perennial hay crop forages or corn crop residues were compared to maintaining cows in a drylot. In the summer of 1992, two cuttings of hay were harvested (June 22 and August 2) from three 10-acre fields containing “Johnstone” endophyte-free tall fescue and “Spreador II” alfalfa, and one cutting of hay was harvested from three 10- acre fields of smooth brome grass. “Arlington” red clover was frost-seeded into the smooth bromegrass fields in 1993 and into tall fescue-alfalfa and smooth bromegrass fields into 1994. Two cuttings of hay were harvested from all fields in subsequent years, and three-year average hay yields for tall fescue-alfalfa and smooth bromegrass-red clover were 4,336 and 3,481 pounds per acre, respectively. Regrowth of the forage following the August hay harvest of each year was accumulated for winter grazing. Following a killing frost in each year, two fields of each stockpiled forage were stocked with cows in midgestation at two acres per cow. Two 10-acre fields of corn crop residues were also stocked at two acres per cow, following the grain harvest. Mean dry matter forage yields at the initiation of grazing were 1,853, 2,173 and 5,797 pounds per acre for fields containing tall fescue-alfalfa, smooth bromegrass-red clover, and cornstalks, respectively. A drylot was stocked with 18 cows in 1992 and 1993 and 10 cows in 1994. All cows were fed hay as necessary to maintain a body condition score of five. During grazing, mean losses of organic matter were -6.4, -7.6, and -10.7 pounds per acre per cow from tall fescue-alfalfa, smooth bromegrass-red clover, and cornstalk fields. Average organic matter loss rates from stockpiled forages due to weathering alone were equal to only 30% of the weathering losses of the corn crop residues. In vitro digestibility of both stockpiled forages and cornstalks decreased at equal rates during grazing each year, with respective annual loss rates of .14, .08, and .06% per day. Cows grazing corn crop residues required an average of 1,321 pounds per cow less hay than cows maintained in the drylot to maintain equivalent body condition during the grazing season. Cows grazing tall fescue-alfalfa or smooth bromegrass-red clover had body weight gains and condition score changes equal to cows maintained in a drylot but required 64% and 62% less harvested hay than cows in the drylot during the grazing season. Over the entire stored forage cows grazing tall fescue-alfalfa and smooth bromegrass-red clover required an average of 2,390 and 2,337 pounds per cow less than those maintained in the drylot. Because less hay was needed to maintain cows grazing stockpiled forages, average annual excesses of 5,629 and 3,868 pounds of hay dry matter per cow remained in the stockpiled tall fescue-alfalfa and smooth bromegrass-red clover systems.

Effects of Chemical Composition on Forage Intake of Heifers Fed Hays of Different Species

Alfalfa, smooth bromegrass, and big bluestem hays harvested at two maturities differing by four weeks were fed at mature-to-immature hay ratios of 1:0, 2:1, 1:2, and 0:1 to yearling heifers in an experiment with a three 4 x 4 Latin square design with 14 day periods. Concentrations of in vitro digestible dry matter and crude protein were greater and concentrations of neutral detergent fiber, acid detergent fiber, and indigestible neutral detergent fiber (determined by either a manual method with a 96 hour incubation or an automated method with a 48 hour incubation) were less in alfalfa hay than in the two grass hays and in smooth bromegrass hay than in big bluestem hay. Concentrations of in vitro digestible dry matter and crude protein decreased whereas those of neutral detergent fiber, acid detergent fiber and indigestible neutral detergent fiber increased with increasing forage maturity. Consumptions of dry matter, digestible dry matter, in vitro digestible dry matter, and crude protein were greater for heifers fed alfalfa hay diets than those fed the two grasses. Consumptions of total neutral detergent fiber and indigestible neutral detergent fiber, determined by the automated method with a 48 hour incubation, were greater by heifers fed diets containing big bluestem than those fed alfalfa or smooth bromegrass diets. Consumptions of acid detergent fiber and indigestible neutral detergent fiber, determined by a manual method with a 96 hour incubation, were greater for heifers fed alfalfa or big bluestem hay diets than those of heifers fed smooth bromegrass diets. Consumption of dry matter, in vivo or in vitro digestible dry matter, crude protein, neutral detergent fiber, acid detergent fiber and automated indigestible neutral detergent fiber decreased as the mature-to-immature hay ratio decreased. Diet digestibility was not affected by forage species, but increased as the mature-toimmature hay ratio decreased. Fecal excretion of dry matter and neutral detergent fiber did not differ between forage species or mature-to-immature hay ratios. Forage dry matter intake expressed as a percentage of body weight was significantly related to the concentrations of in vitro digestible dry matter (r2=.14), crude protein (r2=.17), neutral detergent fiber (r2=.20), and manual indigestible neutral detergent fiber (r2=.18) of the hays and the concentration of digestible dry matter of the diets (r2=.43).

Evaluation of a Year-Round Grazing System: Winter Progress Report

The winter component of a year-round grazing system involving grazing of corn crop residues followed by grazing stockpiled grass-legume forages was compared at the McNay Research Farm with that of the winter component of a minimal land system that maintained cows in drylot. In the summers of 1995 and 1996, two and one cuttings of hay per year were harvested from two 15-acre fields containing “Johnston” low endophtye tall fescue and red clover. Two cuttings of hay in 1995 and one cutting in 1996 were harvested from two 15-acre fields of smooth bromegrass and red clover. Hay yields were 4,236 and 4,600 pounds of dry matter per acre for the tall fescue-red clover in 1995 and 1996, and 2,239 and 2,300 pounds of dry matter per acre for the smooth bromegrass-red clover in 1995 and 1996. Following grain harvest, four 7.5-acre fields containing corn crop residues were stocked with cows at midgestation at an allowance of 1.5 acres per cow. Forage yields at the initiation of corn crop grazing in 1995 and 1996 were 3,757 and 3,551 pounds of dry matter per acre for corn crop residues. Stockpiled forage yields were 1,748 and 2,912 pounds of dry matter for tall fescue-red clover and 1,880 and 2,187 pounds for smooth bromegrass-red clover. Corn crop residues and stockpiled forages were grazed in a strip stocking system. For comparison, 20 cows in 1995 and 16 cows in 1996 were placed in two drylots simultaneously with initiation of corn crop grazing, where they remained throughout the winter and spring grazing periods. Cows maintained in drylots or grazing corn crop residue and stockpiled forages were supplemented with hay as large round bales to maintain a body condition score of five. In both years, no seasonal differences in body weight and body condition score were observed between grazing cows or cows maintained in drylots, but grazing cows required 85% and 98% less harvested hay in years 1 and 2 than cows in drylot during the winter and spring. Because less hay was needed to maintain grazing cows, excesses of 12,354 and 5,244 pounds of hay dry matter per cow in 1995 and 1996 remained in the year-round grazing system. During corn crop grazing, organic matter yield decreased at 23.5 and 28.8 pounds of organic matter per day from grazed areas of corn crop residues in 1995 and 1996. Organic matter losses due to weathering were 6.8, 10.3, and 12.7 pounds per day in corn crop residue, tall fescue-red clover and smooth bromegrass-red clover in 1995 and 12.1, 10.7, and 12.1 in 1996. Organic matter losses from grazed and ungrazed areas of tall fescue-red clover and smooth bromegrass-red clover during stockpiled grazing were 6.9, 6.9, and 2.1, 2.9 in 1995 and 13.4, 4.3, and +6.9, 4.4 pounds per day in 1996.

Evaluation of Stockpiled Berseem Clover and Brown Midrib Sorghum x Sudangrass as Supplements for Grazed Cornstalks in Beef Cow Wintering Systems

Berseem clover and oats were incorporated into a corncorn- oat/berseem clover rotation in 1994 and 1995. Two cuttings of oat-berseem clover hay were harvested during the summer before forage was allowed to stockpile for winter grazing. In 1995, a brown midrib sorghum x sudangrass hybrid was seeded into a field adjacent to a corn field. After corn grain harvest in 1994 and 1995, Charolais x Angus x Simmental cows in midgestation were allotted to replicated fields containing corn crop residues with no complementary forages at 2.5 acres/cow, or corn crop residues and stockpiled berseem clover (2:1) at 2.5 acres/cow to simultaneously graze, or to a drylot. In 1995, cows were allotted to fields containing corn crop residues and brown midrib sorghum x sudangrass (7:3) at 2.5 acres/cow. Berseem clover had greater concentrations of digestible organic matter and crude protein than corn crop residues at the initiation of grazing, but had a more rapid decrease in digestible organic matter concentration than corn crop residues. Brown midrib sorghum x sudangrass forage also had a higher initial concentration of digestible organic matter, but an equal rate of decrease in digestible organic matter concentration to corn crop residues in ungrazed areas of the field. Cows grazing berseem clover with corn crop residues had greater body condition score increases during the first half of the grazing season than cows grazing corn crop residues without complementary forages. Cows grazing corn crop residues without complementary forages required 2,786 and 1,412 less lb hay per cow than cows maintained in a drylot in 1994 and 1995. In 1994, simultaneous grazing of berseem clover with corn crop residues did not reduce hay feeding more than feeding corn crop residues alone. However, in 1995, grazing berseem clover or brown midrib sorghum x sudangrass with corn crop residues reduced the amount of hay required to maintain cows by 358 and 376 lb hay per cow compared with grazing corn crop residues without complementary forage.

Evaluation of Stockpiled Berseem Clover and Brown Midrib Sorghum x Sudangrass as Supplements for Grazed Cornstalks in Beef Cow Wintering Systems

Berseem clover and oats were incorporated into a corn-oat/berseem clover rotation in 1994-1996. Two cuttings of oat-berseem clover hay were harvested during the summer before forage was stockpiled for winter grazing. In 1995, brown midrib sorghum x sudangrass hybrid was seeded into a field adjacent to a corn field. This was repeated in 1996 with a standard sorghum x sudangrass hybrid. After corn harvest in 1994–1996, Charolais x Angus x Simmental cows and heifers in midgestation were allotted to corn crop residue, corn crop residue-berseem clover, and corn crop residue-sorghum x sudangrass fields at 2.5 acres/cow, or to a drylot. Berseem clover had greater concentration of digestible organic matter and crude protein than corn crop residues. Corn crop residue digestible organic matter concentration was lower than berseem clover and the brown midrib sorghum x sudangrass, but was higher than that of the standard sorghum x sudangrass hybrid in 1996. Cows grazing corn crop residues without complementary forages required an average of 2,374 less lb. hay per cow than cows maintained in a drylot in 1994-1996. In 1994 and 1996, simultaneous grazing of berseem clover with corn crop residues did not reduce hay feeding more than feeding corn crop residues alone, yet did significantly reduce the amount of hay needed in 1995 to maintain cows by 358 and 376 lb. hay per cow compared with grazing corn crop residues without complementary forage.

Evaluation of a Year-Round Grazing System: Winter Progress Report

The winter component of a year-round grazing system involving grazing of corn crop residues followed by grazing stockpiled grass legume forages was compared at the McNay Research Farm with that of the winter component of a minimal land system that maintained cows in drylot,. In the summer of 1995, two cuttings of hay were harvested from two 15-acre fields containing “Johnston” endophyte-free tall fescue and red clover, and two cuttings of hay were taken from two 15-acre fields of smooth bromegrass and red clover. Hay yields were 4,236 and 4,600 pounds of dry matter per acre for the tall fescue--red clover and smooth bromegrass--red clover. Following grain harvest four 7.5-acre fields containing corn crop residue were stocked with cows at midgestation at an allowance of 1.5 acres per cow. Forage yields at the initiation of corn crop grazing were 3,766pounds of dry matter per acre for corn crop residue, 1,748 pounds for tall fescue--red clover, and 1,.880 pounds for smooth bromegrass--red clover. Corn crop residues and stockpiled forages were grazed in a strip stocking system. For comparison, 20 cows were placed in two drylots simultaneously to the initiation of corn crop grazing where they remained throughout the winter and spring grazing seasons. Cows maintained in drylot or grazing corn crop residue and stockpiled forages were supplemented with hay as large round bales to maintain a body condition score of five. No seasonal differences in body weight and body condition were observed between grazing cows or cows maintained in drylot, but grazing cows required 87% and 84% less harvested hay than cows in drylot during the winter and spring respectively. Because less hay was needed to maintain grazing cows, an excess of 11,905 and 12,803 pounds of hay dry matter per cow remained in the year-round grazing system. During corn crop grazing, organic matter yield decreased at 27.3 pounds of organic matter per day from grazed areas of corn crop residue. Organic matter losses due to weathering were 9.4, 12.9, and 15.8 pounds per day in corn crop residue, tall fescue-red clover and smooth bromegrass-red clover. Organic matter losses from grazed and ungrazed areas during stockpiled grazing were 7.3 and 6.9 for tall fescue--red clover and 2.1, 2.9 for smooth bromegrass--red clover.

Use of Stockpiled Berseem Clover as a Supplement for Grazed Corn Crop Residues

In the fall of 1994, mature Charolais cross cows in midgestation were allotted to duplicate 15 acre fields containing corn crop residues or a 2-to-1 mixture of corn crop residues and berseem clover planted in 3 strips at an allowance of 2.5 acres/cow for a 140 day wintering season. Similar cows were allotted duplicate drylots. All cows were fed hay as necessary to maintain a body condition score of 5. Cows grazing corn crop residues with or without berseem clover required 2596 pounds less hay per cow than cows maintained in a drylot. There was no difference in the amounts of hay required by cows grazing corn crop residues alone or with berseem clover. Initial organic matter yield of berseem clover was nearly that of corn crop residues and did not decrease as rapidly as corn crop residues. Berseem clover had a higher organic matter digestibility than corn crop residues at the initiation of grazing. Organic matter digestibility of berseem clover, however, decreased more rapidly than corn crop residues because of weathering during the winter.

A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle.

Highland cattle with congenital crop ears have notches of variable size on the tips of both ears. In some cases, cartilage deformation can be seen and occasionally the external ears are shortened. We collected 40 cases and 80 controls across Switzerland. Pedigree data analysis confirmed a monogenic autosomal dominant mode of inheritance with variable expressivity. All affected animals could be traced back to a single common ancestor. A genome-wide association study was performed and the causative mutation was mapped to a 4 Mb interval on bovine chromosome 6. The H6 family homeobox 1 (HMX1) gene was selected as a positional and functional candidate gene. By whole genome re-sequencing of an affected Highland cattle, we detected 6 non-synonymous coding sequence variants and two variants in an ultra-conserved element at the HMX1 locus with respect to the reference genome. Of these 8 variants, only a non-coding 76 bp genomic duplication (g.106720058_106720133dup) located in the conserved region was perfectly associated with crop ears. The identified copy number variation probably results in HMX1 misregulation and possible gain-of-function. Our findings confirm the role of HMX1 during the development of the external ear. As it is sometimes difficult to phenotypically diagnose Highland cattle with slight ear notches, genetic testing can now be used to improve selection against this undesired trait.